Natural history collections as windows on evolutionary processes

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long‐term field studies or from experimental studies in the laboratory, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short timescales in response to presumably strong selective pressures. In some instances, evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations.     

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.     

The development of a digitising service centre for natural history collections

Digitarium is a joint initiative of the Finnish Museum of Natural History and the University of Eastern Finland. It was established in 2010 as a dedicated shop for the large-scale digitisation of natural history collections. Digitarium offers service packages based on the digitisation process, including tagging, imaging, data entry, georeferencing, filtering, and validation. During the process, all specimens are imaged, and distance workers take care of the data entry from the images. The customer receives the data in Darwin Core Archive format, as well as images of the specimens and their labels. Digitarium also offers the option of publishing images through Morphbank, sharing data through GBIF, and archiving data for long-term storage. Service packages can also be designed on demand to respond to the specific needs of the customer. The paper also discusses logistics, costs, and intellectual property rights (IPR) issues related to the work that Digitarium undertakes.     

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.     

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods,challenges, applications,and future directions

Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high‐throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.     

Toward a synthetic understanding of the role of phenology in ecology and evolution

Phenology affects nearly all aspects of ecology and evolution. Virtually all biological phenomena—from individual physiology to interspecific relationships to global nutrient fluxes—have annual cycles and are influenced by the timing of abiotic events. Recent years have seen a surge of interest in this topic, as an increasing number of studies document phenological responses to climate change. Much recent research has addressed the genetic controls on phenology, modelling techniques and ecosystem-level and evolutionary consequences of phenological change. To date, however, these efforts have tended to proceed independently. Here, we bring together some of these disparate lines of inquiry to clarify vocabulary, facilitate comparisons among habitat types and promote the integration of ideas and methodologies across different disciplines and scales. We discuss the relationship between phenology and life history, the distinction between organismal- and population-level perspectives on phenology and the influence of phenology on evolutionary processes, communities and ecosystems. Future work should focus on linking ecological and physiological aspects of phenology, understanding the demographic effects of phenological change and explicitly accounting for seasonality and phenology in forecasts of ecological and evolutionary responses to climate change.     

Awareness and use of biodiversity collections by fish biologists

A survey of 280 fish biologists from a diverse pool of disciplines was conducted in order to assess the use made of biodiversity collections and how collections can better collect, curate and share the data they have. From the responses, data for how fish biologists use collections, what data they find the most useful, what factors influence the decisions to use collections, how they access the data and explore why some fish biologists make the decision to not use biodiversity collections is collated and reported. The results of which could be used to formulate sustainability plans for collections administrators and staff who curate fish biodiversity collections, while also highlighting the diversity of data and uses to researchers.     

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.     

Life history of Xenodexia ctenolepis: implications for life history evolution in the family Poeciliidae

Xenodexia ctenolepis (Hubbs, 1950) is a uniquely asymmetrical species in the fish family Poeciliidae that is endemic to a remote region of Guatemala. In the present study, we describe its life history based on the dissection of 65 adult females from three different collections. We show that it is a livebearer, has superfetation, or the ability to carry multiple litters of young in different stages of development, and has matrotrophy, or placentation, which results in the dry mass of young at birth being three- to four-fold greater than the egg at fertilization. The size distribution of males is non-normal in a fashion that suggests a genetic polymorphism for age and size at maturity. Most phylogenies place Tomeurus gracilis as the sister taxon to the remaining members of the family Poeciliidae. Because Tomeurus is the sole egg-layer in the family, egg-laying is thought to represent the life history of the common ancestor. Because Xenodexia possesses three supposed derived traits (livebearing, superfetation and matrotrophy), this phylogenetic hypothesis suggests that Xenodexia has a highly derived life history with respect to other members of the family. By contrast, the most recent DNA-based phylogeny suggests Xenodexia is the sister taxon to the remainder of the family. If this proves to be true, it suggests that some or all of these life history traits may have been characteristic of the common ancestor to the family, then lost and re-evolved multiple times within the family.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 77–85.     

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.     

Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana

Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment‐specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2‐5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.     

Patrick Matthew's law of natural selection

Patrick Matthew is the little‐known first originator of macroevolution by natural selection. I review his ideas, and introduce some previously unnoticed writings (catalogued at a new website: http://smarturl.it/patrickmatthew ) that clarify how they differ from Darwin's and Wallace's. Matthew's formulation emphasized natural selection as an axiomatic ‘law’ rather than a ‘theory’, a distinction that could still be of use to us today. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●● , ●●–●●.     

Scientific natural history: a key base to ecology

Like all science, ecology depends upon an observational and experimental base. This is 'scientific natural history': it is a tradition particularly strong in Britain, where it is nurtured and stimulated in local and national natural history societies. Ecology in Britain sprang directly from natural history, in contrast to its origins in other countries from physiology. It is argued that a healthy ecology depends on a nourishing knowledge of field biology.     

Life history of wild Sumatran orangutans (Pongo abelii)

We present life history data on wild Sumatran orangutans gleaned from a 32-year and a 5.5-year study. Estimated age at first reproduction was 15.4 years. At 9.3 years, the average interbirth interval for this population is the longest ever recorded for any great ape population, significantly longer than that of a Bornean orangutan population. We find that age-specific mortality of Sumatran orangutans does not differ between sexes and is significantly lower than that of wild chimpanzees. We conclude that orangutan life history is the slowest among extant great apes. In accordance with their slow life history, longevity in the wild is estimated to be at least 58 years for males and at least 53 for females. We find no evidence for menopause. These data suggest that compared to the ancestral state, humans have undergone less of an increase in longevity than commonly assumed, and have experienced selection on earlier cessation of reproduction.     

Evolution of quantitative traits in the wild: mind the ecology

Recent advances in the quantitative genetics of traits in wild animal populations have created new interest in whether natural selection, and genetic response to it, can be detected within long-term ecological studies. However, such studies have re-emphasized the fact that ecological heterogeneity can confound our ability to infer selection on genetic variation and detect a population''s response to selection by conventional quantitative genetics approaches. Here, I highlight three manifestations of this issue: counter gradient variation, environmentally induced covariance between traits and the correlated effects of a fluctuating environment. These effects are symptomatic of the oversimplifications and strong assumptions of the breeder''s equation when it is applied to natural populations. In addition, methods to assay genetic change in quantitative traits have overestimated the precision with which change can be measured. In the future, a more conservative approach to inferring quantitative genetic response to selection, or genomic approaches allowing the estimation of selection intensity and responses to selection at known quantitative trait loci, will provide a more precise view of evolution in ecological time.     

Life history evolution of seed-bank annuals in response to seed predation

Summary We present a model of life history evolution for seed-bank annuals in temporally varying environments in which both the seed bank and the distribution of fecundity across year types evolve in response to seed predation. The fecundity distribution refers to the expected reproductive success of germinating seeds across a range of different year types. We assume that it is a function of traits pertaining to growth and survival under different environmental circumstances. Such traits are assumed to result in a trade-off between reproduction in favourable and less favourable years. The model is used to explore how seed predation selects for changes in the seed bank and fecundity distribution and how changes in each of these further select for changes in the other. The direction of selection is contingent upon: whether or not a seed bank exists; whether predation has a greater effect on fresh or buried seed; whether the predation rate differs in different year types, and if so, if it is positively or negatively density-dependent; whether or not predation rate is sensitive to individual variation in seed yield, and if so, whether and how such dependency varies in different kinds of year. Under a variety of predation regimes, seed predators select for a temporal clumping of reproduction; i.e. a specialisation on a favourable subset of year types. This effect usually requires negatively density-dependent seed predation of the sort created by predator satiation. In fact, the classic scenario favouring masting in perennials creates the strongest such effect in our model. Yet unlike the masting of perennial plants, this effect is favoured in a seed-bank annual. It can even occur in a strict annual without a seed bank, and it can occur in a seed-bank annual even if seed predation is density-independent.     

Eco‐evolutionary dynamics in response to selection on life‐history

Understanding the consequences of environmental change on ecological and evolutionary dynamics is inherently problematic because of the complex interplay between them. Using invertebrates in microcosms, we characterise phenotypic, population and evolutionary dynamics before, during and after exposure to a novel environment and harvesting over 20 generations. We demonstrate an evolved change in life‐history traits (the age‐ and size‐at‐maturity, and survival to maturity) in response to selection caused by environmental change (wild to laboratory) and to harvesting (juvenile or adult). Life‐history evolution, which drives changes in population growth rate and thus population dynamics, includes an increase in age‐to‐maturity of 76% (from 12.5 to 22 days) in the unharvested populations as they adapt to the new environment. Evolutionary responses to harvesting are outweighed by the response to environmental change (~ 1.4 vs. 4% change in age‐at‐maturity per generation). The adaptive response to environmental change converts a negative population growth trajectory into a positive one: an example of evolutionary rescue.