Genomics of natural history collections for understanding evolution in the wild

A long‐standing question in biology is how organisms change through time and space in response to their environment. This knowledge is of particular relevance to predicting how organisms might respond to future environmental changes caused by human‐induced global change. Usually researchers make inferences about past events based on an understanding of current static genetic patterns, but these are limited in their capacity to inform on underlying past processes. Natural history collections (NHCs) represent a unique and critical source of information to provide temporally deep and spatially broad time‐series of samples. By using NHC samples, researchers can directly observe genetic changes over time and space and link those changes with specific ecological/evolutionary events. Until recently, such genetic studies were hindered by the intrinsic challenges of NHC samples (i.e. low yield of highly fragmented DNA). However, recent methodological and technological developments have revolutionized the possibilities in the novel field of NHC genomics. In this Special Feature, we compile a range of studies spanning from methodological aspects to particular case studies which demonstrate the enormous potential of NHC samples for accessing large genomic data sets from the past to advance our knowledge on how populations and species respond to global change at multiple spatial–temporal scales. We also highlight possible limitations, recommendations and a few opportunities for future researchers aiming to study NHC genomics.     

No specimen left behind: industrial scale digitization of natural history collections

Traditional approaches for digitizing natural history collections, which include both imaging and metadata capture, are both labour- and time-intensive. Mass-digitization can only be completed if the resource-intensive steps, such as specimen selection and databasing of associated information, are minimized. Digitization of larger collections should employ an “industrial” approach, using the principles of automation and crowd sourcing, with minimal initial metadata collection including a mandatory persistent identifier. A new workflow for the mass-digitization of natural history museum collections based on these principles, and using SatScan® tray scanning system, is described.     

Combining allele frequency and tree‐based approaches improves phylogeographic inference from natural history collections

Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set and determine what proportion of the total support the top‐ranked model garners, we conduct model selection using two analytical approaches—allele frequency‐based, implemented in fastsimcoal2 , and gene tree‐based, implemented in phrapl . We then expand this model selection framework by including an assessment of absolute fit of the models to the data. For this, we utilize DNA isolated from existing natural history collections that span the distribution of red alder (Alnus rubra) in the Pacific Northwest of North America to generate genomic data for the evaluation of 13 demographic scenarios. The quality of DNA recovered from herbarium specimen leaf tissue was assessed for its utility and effectiveness in demographic model selection, specifically in the two approaches mentioned. We present strong support for the use of herbarium tissue in the generation of genomic DNA, albeit with the inclusion of additional quality control checks prior to library preparation and analyses with multiple approaches that incorporate various data. Analyses with allele frequency spectra and gene trees predominantly support A. rubra having experienced an ancient vicariance event with intermittent and frequent gene flow between the disjunct populations. Additionally, the data consistently fit the most frequently selected model, corroborating the model selection techniques. Finally, these results suggest that the A. rubra disjunct populations do not represent separate species.     

Whole-drawer imaging for digital management and curation of a large entomological collection

Whole-drawer imaging is shown to be an effective tool for rapid digitisation of large insect collections. On-line, Whole-drawer images facilitate more effective collection management, virtual curation, and public engagement. The Whole-drawer imaging experience at the Australian National Insect Collection is discussed, with an explanation of workflow and examples of benefits.     

The natural history of the ethical concept and its implications for the present natural equilibrium

The present article was originally published in the medical italian journal,Rassegna Medica, 1984. The author, on the basis of the recent development of the biotechnology, genetic engineering and environment exploitation by man, attempts to reconstruct the natural history of the ethical concept and its implications for the present natural equilibrium. On this basis he suggests a concept of bioethics which stresses Man-Environment interaction.     

Comparative genetic analyses of historical and contemporary collections highlight contrasting demographic histories for the bumble bees Bombus pensylvanicus and B. impatiens in Illinois

Direct comparison of genetic patterns between museum specimens and contemporary collections can be a powerful approach for detecting recent demographic changes. Using microsatellite markers, we examined historical and contemporary genetic variation from an apparently declining bumble bee species, Bombus pensylvanicus , and from a stable species, Bombus impatiens , in central Illinois. For each species, we genotyped specimens from the Illinois Natural History Survey collected from three populations between 1969–1972 and from a resurvey of the same areas conducted in 2008. Population structure in B . pensylvanicus increased markedly over the last four decades (from θ_ST = 0.001 to 0.027) while no structure was detected in B . impatiens for either time period (θ_ST = –0.006 to –0.003). Changes in genetic diversity were not significant for either species, although small reductions were observed for B . pensylvanicus in all three populations. Coalescent simulations incorporating both contemporary and historical samples suggest that this small change is not surprising for recent population declines, as large reductions in genetic diversity were only apparent under the most severe bottleneck scenarios. These results demonstrate how comparisons of genetic patterns between temporal periods and species can help elucidate potential threats to population health and suggest several strategies that might be useful in the conservation of B . pensylvanicus in the Midwestern USA.     

Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation

Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200‐year‐old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813–1861) was strongly reduced in descendants (1923–1940) during the mid‐19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant‐sized (managed) population. Differentiation was high among periods (F_ST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D‐loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population.     

中国微生物学会微生物资源专业委员会发展历程北大核心

中国微生物学会微生物资源专业委员会成立于2009年,致力于推动微生物资源科研工作的开展,为微生物资源的保护与可持续利用提供技术支撑和战略指导。积极开展各种形式的学术交流、人才培养和国际合作,促进微生物资源领域的创新与发展,推动我国微生物学科的不断进步。随着科技的不断进步和经济的快速发展,微生物资源的研究和利用已成为国际科技领域的重要热点之一。因此,微生物资源专业委员会的建设与发展具有重要意义,将进一步推动我国微生物学科的发展,提高我国在该领域的学术地位和国际竞争力。     

The genomic and physiological basis of life history variation in a butterfly metapopulation

Unravelling the mechanisms underlying variation in life history traits is of fundamental importance for our understanding of adaptation by natural selection. While progress has been made in mapping fitness-related phenotypes to genotypes, mainly in a handful of model organisms, functional genomic studies of life history adaptations are still in their infancy. In particular, despite a few notable exceptions, the genomic basis of life history variation in natural populations remains poorly understood. This is especially true for the genetic underpinnings of life history phenotypes subject to diversifying selection driven by ecological dynamics in patchy environments--as opposed to adaptations involving strong directional selection owing to major environmental changes, such as latitudinal gradients, extreme climatic events or transitions from salt to freshwater. In this issue of Molecular Ecology,Wheat et al. (2011) now make a significant leap forward by applying the tools of functional genomics to dispersal-related life history variation in a butterfly metapopulation. Using a combination of microarrays, quantitative PCR and physiological measurements, the authors uncover several metabolic and endocrine factors that likely contribute to the observed life history phenotypes. By identifying molecular candidate mechanisms of fitness variation maintained by dispersal dynamics in a heterogeneous environment,they also begin to address fascinating interactions between the levels of physiology, ecology and evolution.     

The development and demise of a Medieval forest-meadow system at Linnaeus' birthplace in southern Sweden: implications for conservation and forest history

The rapid industrialisation of agriculture and forestry during the last century has contributed to a transformation of the forested landscape in southern Sweden. Palaeoecological investigation revealed how the Medieval forest-meadow system was created about 900 years ago from a deciduous forest type that had been rather stable for the previous 3000 years. The study site was a forest hollow close to where Linnaeus was born and brought up. The species-rich forest-meadow system suffered from over-grazing during the human-population peak of the nineteenth century, and was abandoned about one hundred years ago. The recent forest succession in southern Sweden has led to reduced floristic biodiversity and created conservation problems related to disappearance of open landscape, even though the remnant vegetation is moving towards the near-natural forest type. Spatially detailed palaeoecology permits documentation of baseline conditions, and places conservation debates in a valuable temporal perspective.     

The potential for automating assisted natural regeneration of tropical forest ecosystems

Assisted (or accelerated) natural regeneration (ANR) will play an important role in meeting the UN target to restore forest to 350 million hectares of degraded land, by 2030. However, since most accessible land is already used for agriculture, most of the sites, available for ANR, are far from roads and/or on difficult terrain, where implementing ANR with human labour is not practical. Therefore, this paper explores the potential of emerging technologies, such as low‐cost UAVs (drones) and new imaging devices, to automate ANR tasks, including site monitoring (to assess site potential for natural regeneration, plan interventions and assess progress), maintenance of natural regeneration (particularly weeding) and species enrichment through aerial seeding. The usefulness of existing technologies is reviewed and future innovations needed, to provide practicable support for ANR, are discussed. Intensive collaboration, among technologists and forest ecologists, will be essential to ensure that technological innovations are based firmly on sound restoration science.     

Evolution of natural history information in the 21st century – developing an integrated framework for biological and geographical data

Threats to marine and estuarine species operate over many spatial scales, from nutrient enrichment at the watershed/estuarine scale to invasive species and climate change at regional and global scales. To help address research questions across these scales, we provide here a standardized framework for a biogeographical information system containing queriable biological data that allows extraction of information on multiple species, across a variety of spatial scales based on species distributions, natural history attributes and habitat requirements. As scientists shift from research on localized impacts on individual species to regional and global scale threats, macroecological approaches of studying multiple species over broad geographical areas are becoming increasingly important. The standardized framework described here for capturing and integrating biological and geographical data is a critical first step towards addressing these macroecological questions and we urge organizations capturing biogeoinformatics data to consider adopting this framework.     

Intraperitoneal delivery of human natural killer cells for treatment of ovarian cancer in a mouse xenograft model

Background aimsThere is an urgent need for novel therapeutic strategies for relapsed ovarian cancer. Dramatic clinical anti-tumor effects have been observed with interleukin (IL)-2 activated natural killer (NK) cells; however, intravenous delivery of NK cells in patients with ovarian cancer has not been successful in ameliorating disease. We investigated in vivo engraftment of intraperitoneally (IP) delivered NK cells in an ovarian cancer xenograft model to determine if delivery mode can affect tumor cell killing and circumvent lack of NK cell expansion.MethodsAn ovarian cancer xenograft mouse model was established to evaluate efficacy of IP-delivered NK cells. Tumor burden was monitored by bioluminescent imaging of luciferase-expressing ovarian cancer cells. NK cell persistence, tumor burden and NK cell trafficking were evaluated. Transplanted NK cells were evaluated by flow cytometry and cytotoxicity assays.ResultsIP delivery of human NK cells plus cytokines led to high levels of circulating NK and was effective in clearing intraperitoneal ovarian cancer burden in xenografted mice. NK cells remained within the peritoneal cavity 54 days after injection and had markers of maturation. Additionally, surviving NK cells were able to kill ovarian cancer cells at a rate similar to pre-infusion levels, supporting that in vivo functionality of human NK cells can be maintained after IP infusion.ConclusionsIP delivery of NK cells leads to stable engraftment and antitumor response in an ovarian cancer xenograft model. These data support further pre-clinical and clinical evaluation of IP delivery of allogeneic NK cells in ovarian cancer.     

The impact of transgenic plants on natural enemies: a critical review of laboratory studies

We reviewed laboratory tests which studied the impact of genetically modified plants on arthropod natural enemies. A total of 18 species of predators and 14 species of parasitoids have been tested, most in only a few experiments. Certain groups (braconid wasps) or species (the green lacewing, Chrysoperla carnea) have attracted much effort, while representatives of others, including whole orders (e.g., Diptera), have never had a species tested. We conclude that laboratory tests are not the ‘worst case’ scenarios intended by the experimental designs, and are not often ecologically realistic: they typically provided ad libitum feeding, no prey choice, single prey type, no combination of stress factors and usually uniform temperatures. None of these are representative of field conditions, yet most could be easily mimicked in more complex laboratory tests. In most cases (94.6%), the studies were unable to indicate the level of power required to detect any impact. Small sample size and large variability are factors that mask all but very large differences in potential effects. For predators, 126 parameters were quantified, most commonly including survival/mortality (37 cases), development time (22), and body mass/size (20). For parasitoids, 128 parameters were quantified, the majority involving lectins or proteinase inhibitors. Most frequent measurements were: fecundity (23 experiments), adult longevity, extent of parasitism (17 each), body size, mortality, and larval development time. An aggregative scoring (summarising all quantified parameters) indicated that the laboratory tests quantified a remarkable number of cases (30% for predators, 39.8% for parasitoids), where the impacts of the genetically modified plant were significantly negative. These involve various parameters, organisms, test methods, and significance levels, but collectively they indicate that the use of genetically modified crops may result in negative effects on the natural enemies of crop pests.     

The predictability and magnitude of life‐history divergence to ecological agents of selection: a meta‐analysis in livebearing fishes

Environments causing variation in age‐specific mortality – ecological agents of selection – mediate the evolution of reproductive life‐history traits. However, the relative magnitude of life‐history divergence across selective agents, whether divergence in response to specific selective agents is consistent across taxa and whether it occurs as predicted by theory, remains largely unexplored. We evaluated divergence in offspring size, offspring number, and the trade‐off between these traits using a meta‐analysis in livebearing fishes (Poeciliidae). Life‐history divergence was consistent and predictable to some (predation, hydrogen sulphide) but not all (density, food limitation, salinity) selective agents. In contrast, magnitudes of divergence among selective agents were similar. Finally, there was a negative, asymmetric relationship between offspring‐number and offspring‐size divergence, suggesting greater costs of increasing offspring size than number. Ultimately, these results provide strong evidence for predictable and consistent patterns of reproductive life‐history divergence and highlight the importance of comparing phenotypic divergence across species and ecological selective agents.     

The indigenous honey bees of Saudi Arabia (Hymenoptera, Apidae, Apis mellifera jemenitica Ruttner): Their natural history and role in beekeeping

Apis mellifera jemenitica Ruttner (= yemenitica auctorum: videEngel 1999) has been used in apiculture throughout the Arabian Peninsula since at least 2000 BC. Existing literature demonstrates that these populations are well adapted for the harsh extremes of the region. Populations of Apis mellifera jemenitica native to Saudi Arabia are far more heat tolerant than the standard races often imported from Europe. Central Saudi Arabia has the highest summer temperatures for the Arabian Peninsula, and it is in this region where only Apis mellifera jemenitica survives, while other subspecies fail to persist. The indigenous race of Saudi Arabia differs from other subspecies in the region in some morphological, biological, and behavioral characteristics. Further taxonomic investigation, as well as molecular studies, is needed in order to confirm whether the Saudi indigenous bee populations represent a race distinct from Apis mellifera jemenitica, or merely an ecotype of this subspecies.     

自然公园功能分区方法研究——以黄山风景名胜区为例

为了推进生态文明和美丽中国建设,合理利用自然资源,促进人与自然的和谐,我国提出"国家公园体制"并要求对保护地体系进行优化完善。功能分区作为保护地规划与管理中最相关的过程,是保护地体系优化的重要方面。自然公园作为多类型保护地的一个组成部分,其功能分区还存在着对生态与经济协调发展考虑不充分,缺乏综合性的分区研究等问题,不利于保护地的可持续发展。因此,为了推进保护地体系的优化与完善,从综合管理的角度出发,基于不可替代性、生态脆弱性、景观资源评价和经济建设的适宜性等方面提出了自然公园的功能分区方法,并以黄山风景名胜区为例进行了分区研究。本研究认为,自然公园的功能分区可包括生态保育区、景观保护区和经济发展区三个一级区,生态保育区可以分为核心生态保育区和重要生态保育区,景观保护区可以分为核心景观保护区和重要景观保护区,经济发展区可以分为游憩区、农业区和居住区。