Contribution of genetics and genomics to seagrass biology and conservation

Genetic diversity is one of three forms of biodiversity recognized by the IUCN as deserving conservation along with species and ecosystems. Seagrasses provide all three levels in one. This review addresses the latest advances in our understanding of seagrass population genetics and genomics within the wider context of ecology and conservation. Case studies are used from the most widely studied, northern hemisphere species Zostera marina, Z. noltii, Posidonia oceanica and Cymodocea nodosa.

We begin with an analysis of the factors that have shaped population structure across a range of spatial and temporal scales including basin-level phylogeography, landscape-scale connectivity studies, and finally, local-scale analyses at the meadow level—including the effects of diversity, clonality and mating system. Genetic diversity and clonal architecture of seagrass meadows differ within and among species at virtually all scales studied. Recent experimental studies that have manipulated seagrass genetic biodiversity indicate that genotypic diversity matters in an immediate ecological context, and enhances population growth, resistance and resilience to perturbation, with positive effects on abundance and diversity of the larger community. In terms of the longer term, evolutionary consequences of genetic/genotypic diversity in seagrass beds, our knowledge remains meagre. It is here that the new tools of ecogenomics will assist in unravelling the genetic basis for adaptation to both biotic and abiotic change. Gene expression studies will further assist in the assessment of physiological performance which may provide an early warning system under complex disturbance regimes that seagrasses are at or near their tolerance thresholds.

At the most fundamental level, ecological interactions of seagrasses with their environment depends on the genetic architecture and response diversity underlying critical traits. Hence, given the rapid progress in data acquisition and analysis, we predict an increasing role of genetic and genomic tools for seagrass ecology and conservation.     

遗传学与基因组学整合课程探讨

基因组学是遗传学的重要学科分支,具有全新研究思维和技术手段,已经形成一个系统而完整的体系。在本科课程中加强基因组学教学是遗传学学科发展的要求,有利于对学生进行科学思维训练、提高学生生物伦理学修养和学习兴趣。整合遗传学与基因组学课程符合学科发展规律和教学规律。目前国内已经基本具备相关教材,通过调整遗传学教学内容,合理选择教学方法,充分利用计算机辅助教学,在本科教学中整合遗传学与基因组学是可行的。     

Microsatellite markers for population and conservation genetics of tropical trees

We have developed microsatellite or simple sequence repeat (SSR) genetic markers for the tropical tree Pithecellobium elegans (Mimosoideae). The frequency of this class of marker is estimated and the level and distribution of variability at these markers is assessed and contrasted to that found at isozyme markers in the same populations. The results indicate that SSR loci are powerful tools for the analysis of population structure and that, in these populations, they provide a means of accurately examining two important parameters in conservation biology, gene flow and paternity.     

Conservation genetics and genomics of threatened vertebrates in China

Conservation genetics and genomics are two independent disciplines that focus on using new techniques in genetics and genomics to solve problems in conservation biology. During the past two decades, conservation genetics and genomics have experienced rapid progress. Here, we summarize the research advances in the conservation genetics and genomics of threatened vertebrates (e.g., carnivorans, primates, ungulates, cetaceans, avians, amphibians and reptiles) in China. First, we introduce the concepts of conservation genetics and genomics and their development. Second, we review the recent advances in conservation genetics research, including noninvasive genetics and landscape genetics. Third, we summarize the progress in conservation genomics research, which mainly focuses on resolving genetic problems relevant to conservation such as genetic diversity, genetic structure, demographic history, and genomic evolution and adaptation. Finally, we discuss the future directions of conservation genetics and genomics.     

Population genomics of the inbred Scandinavian wolf

The Scandinavian wolf population represents one of the genetically most well-characterized examples of a severely bottlenecked natural population (with only two founders), and of how the addition of new genetic material (one immigrant) can at least temporarily provide a 'genetic rescue'. However, inbreeding depression has been observed in this population and in the absence of additional immigrants, its long-term viability is questioned. To study the effects of inbreeding and selection on genomic diversity, we performed a genomic scan with approximately 250 microsatellite markers distributed across all autosomes and the X chromosome. We found linkage disequilibrium (LD) that extended up to distances of 50 Mb, exceeding that of most outbreeding species studied thus far. LD was particularly pronounced on the X chromosome. Overall levels of observed genomic heterozygosity did not deviate significantly from simulations based on known population history, giving no support for a general selection for heterozygotes. However, we found evidence supporting balancing selection at a number of loci and also evidence suggesting directional selection at other loci. For markers on chromosome 23, the signal of selection was particularly strong, indicating that purifying selection against deleterious alleles may have occurred even in this very small population. These data suggest that population genomics allows the exploration of the effects of neutral and non-neutral evolution on a finer scale than what has previously been possible.     

Advancing ecological understandings through technological transformations in noninvasive genetics

Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used for wildlife studies since the 1990s, technological advances continue to make noninvasive approaches among the most used and rapidly advancing areas in genetics. Here, we review recent advances in noninvasive genetics and how they allow us to address important research and management questions thanks to improved techniques for DNA extraction, preservation, amplification and data analysis. We show that many advances come from the fields of forensics, human health and domestic animal health science, and suggest that molecular ecologists explore literature from these fields. Finally, we discuss how the combination of advances in each step of a noninvasive genetics study, along with fruitful areas for future research, will continually increase the power and role of noninvasive genetics in molecular ecology and conservation genetics.     

Historical perspectives on population genetics and conservation of three marine turtle species

Considerable phylogeographic and population genetic research has been conducted on marine turtles. Less attention, however, has been paid to the historical patterns and processes that have led to present patterns of genetic structure, and particularly, how these populations have responded to major climatic changes in the past. To address these questions, we analyzed previously published mitochondrial haplotype data independently for three marine turtle species, the loggerhead (Caretta caretta), hawksbill (Eretmochelys imbricata), and green turtle (Chelonia mydas). Considering all three species, we conducted analyses on a total of 657 individuals from 36 nesting beaches in the Atlantic and Mediterranean. Our results suggest that much of the contemporary genetic structure has been significantly affected by complex patterns of historical population subdivision, long-distance dispersal, and restricted geneflow. These inferences also imply that the climatic and sea level fluctuations during the Pleistocene may have had contrasting effects on genetic structure (e.g., fragmenting versus homogenizing) and on population sizes. Estimates of historical and current effective population sizes further highlight differential demographic responses across species to historical climatic cycles. Collectively, our results provide evidence for the occurrence of historical refugia through climatic cycles and complex historical metapopulation dynamics, and identify common and unique patterns of metapopulation structure across species. These historical patterns provide a basis for predictive estimates of metapopulation responses to habitat loss, population extirpation, and global climatic change.     

Reproductive biology in the era of genomics biology

Current and emerging technologies in reproductive biology, including assisted reproductive technologies and animal cloning, are discussed in the context of the impact of genomics era biology. The discussion focuses on the endocrinology associated with establishment and maintenance of pregnancy, fetal-placental development, lactation, and neonatal survival. Various aspects of uterine biology, including development during the neonatal period and function in adult females, are discussed with respect to reproductive efficiency. It is clear that combining strategies for use of conventional animal models for studying the reproductive system with new genomics technologies will provide exceptional opportunities in discovery research involving data integration and application of functional genomics to benefit animal agriculture and the biomedical community. New and emerging biotechnologies and comparative genomics approaches will greatly advance our understanding of genes that are critical to development of the reproductive system and to key events at each stage of the reproductive cycle of females and males.     

Evolutionary biology and practical conservation: bridging a widening gap

At the ecosystem, species and population level, available measures suggest that average rates of loss of populations and habitats are now around 1% per year and seem likely to increase in the future. Habitat conversion continues in most parts of the world, especially in areas of high species richness, and novel threats, especially climate change, will pose new challenges. With this pressure, maintaining evolutionary processes in natural populations will be critical to longer term persistence, and will often require specific planning relevant to the context. However, in many areas of policy and practice, urgent actions tend to focus on pattern-based analyses and considerations of evolutionary and ecological processes are neglected. At a variety of levels, from setting goals to implementing conservation management at the site or species level, there are simple adjustments that can be made. Improved methods for integrating the work of scientists and policymakers is recommended, from the beginning to end of the planning process.     

Functional genomics in the post-genome era

As the biomedical research community enters the post-genome era, studying gene expression patterns and phenotypes in model organisms will be an important part of analyzing the role of genes in human health and disease. New technologies involving DNA chips will improve the ability to evaluate the differential expression of a large number of genes simultaneously. Also, new approaches for generating mutations in mice will significantly decrease the cost and increase the rate of generating mutant lines that model human disease.     

Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae)

Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal-river homing. Overall, the DNA data show that P. expansa populations lack a long history of genetic differentiation, but that each major tributary currently forms a semi-isolated reproductive population and should be managed accordingly.     

Vegetable biology and breeding in the genomics era

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

     

Integrating floral scent, pollination ecology and population genetics

1 . Floral scent is a key factor in the attraction of pollinators. Despite this, the role of floral scent in angiosperm speciation and evolution remains poorly understood. Modern population genetic approaches when combined with pollination ecology can open new opportunities for studying the evolutionary role of floral scent.
2 . A framework of six hypotheses for the application of population genetic tools to questions about the evolutionary role of floral scent is presented. When floral volatile chemistry is linked to pollinator attraction we can analyse questions such as: Does floral volatile composition reflect plant species boundaries? Can floral scent facilitate or suppress hybridization between taxa? Can the attraction of different pollinators influence plant mating systems and pollen-mediated gene flow? How is population genetic structure indirectly influenced by floral scent variation?
3 . The application of molecular tools in sexually deceptive orchids has confirmed that volatile composition reflects species boundaries, revealed the role of shared floral odour in enabling hybridization, confirmed that the sexual attraction mediated by floral odour has implications for pollen flow and population genetic structure and provided examples of pollinator-mediated selection on floral scent variation. Interdisciplinary studies to explore links between floral volatile variation, ecology and population genetics are rare in other plant groups.
4 . Ideal study systems for future floral scent research that incorporate population genetics will include closely related taxa that are morphologically similar, sympatric and co-flowering as well as groups that display wide variation in pollination mechanisms and floral volatiles.     

Opening sequence: computational genomics in the era of high-throughput sequencing

A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011.     

Toward a new synthesis: population genetics and evolutionary developmental biology

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.