Keith David Bennett

How biodiversity is changing in our time represents a major concern for all organismal biologists. Anthropogenic changes to our planet are decreasing species diversity through the negative effects of pollution, habitat destruction, direct extirpation of species, and climate change. But major biotic changes—including those that have both increased and decreased species diversity—have happened before in Earth’s history. Biodiversity dynamics in past eras provide important context to understand ecological responses to current environmental change. The work of assessing biodiversity is woven into ecology, environmental science, conservation, paleontology, phylogenetics, evolutionary and developmental biology, and many other disciplines; yet, the absolute foundation of how we measure species diversity depends on taxonomy and systematics. The aspiration of this symposium, and complementary contributed talks, was to promote better understanding of our common goals and encourage future interdisciplinary discussion of biodiversity dynamics. The contributions in this collection of papers bring together a diverse group of speakers to confront several important themes. How can biologists best respond to the urgent need to identify and conserve diversity? How can we better communicate the nature of species across scientific disciplines? Where are the major gaps in knowledge about the diversity of living animal and plant groups, and what are the implications for understanding potential diversity loss? How can we effectively use the fossil record of past diversity and extinction to understand current biodiversity loss?

A genus is a taxonomic unit that may contain one species (monotypic) or thousands. Yet counts of genera or families are used to quantify diversity where species-level data are not available. High frequencies of monotypic genera (~30% of animals) have previously been scrutinized as an artefact of human classification. To test whether Linnean taxonomy conflicts with phylogeny, we compared idealized phylogenetic systematics in silico with real-world data. We generated highly replicated, simulated phylogenies under a variety of fixed speciation/extinction rates, imposed three independent taxonomic sorting algorithms on these clades (2.65 × 10⁸ simulated species) and compared the resulting genus size data with quality-controlled taxonomy of animal groups (2.8 × 10⁵ species). ‘Perfect’ phylogenetic systematics arrives at similar distributions to real-world taxonomy, regardless of the taxonomic algorithm. Rapid radiations occasionally produce a large genus when speciation rates are favourable; however, small genera can arise in many different ways, from individual lineage persistence and/or extinctions creating subdivisions within a clade. The consistency of this skew distribution in simulation and real-world data, at sufficiently large samples, indicates that specific aspects of its mathematical behaviour could be developed into generalized or nomothetic principles of the global frequency distributions of higher taxa. Importantly, Linnean taxonomy is a better-than-expected reflection of underlying evolutionary patterns.

Contents Summary 924 I. Introduction 925 II. Environmental and temporal limits for survival of aDNA 925 III. Lake sediments 927 IV. Perspective for plant aDNA research 929 V. Perspective for plant aDNA research 930 VI. Pollen DNA 930 VII. Sedimentary aDNA 931 VIII. Recent key findings and future methods using HTS techniques 933 IX. Challenges when studying aDNA from lake sediments 935 X. Bioinformatic processing 936 XI. Conclusions and directions for future research 938 Acknowledgements 938 References 938 Summary: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.

Smith et al. (Reports, 27 February 2015, p. 998) identify wheat DNA from an 8000-calendar-years-before-the-present archaeological site in southern England and conclude that wheat was traded to Britain 2000 years before the arrival of agriculture. The DNA samples are not dated, either directly or from circumstantial evidence, so there is no chronological evidence to support the claim.

We describe the career of John Birks as a pioneering scientist who has, over a career spanning five decades, transformed palaeoecology from a largely descriptive to a rigorous quantitative science relevant to contemporary questions in ecology and environmental change. We review his influence on students and colleagues not only at Cambridge and Bergen Universities, his places of primary employment, but also on individuals and research groups in Europe and North America. We also introduce the collection of papers that we have assembled in his honour. The papers are written by his former students and close colleagues and span many of the areas of palaeoecology to which John himself has made major contributions. These include the relationship between ecology and palaeoecology, late-glacial and Holocene palaeoecology, ecological succession, climate change and vegetation history, the role of palaeoecological techniques in reconstructing and understanding the impact of human activity on terrestrial and freshwater ecosystems and numerical analysis of multivariate palaeoecological data.

Summary: Pollen grains are microscopic so their identification and quantification has, for decades, depended upon human observers using light microscopes: a labour‐intensive approach. Modern improvements in computing and imaging hardware and software now bring automation of pollen analyses within reach. In this paper, we provide the first review in over 15 yr of progress towards automation of the part of palynology concerned with counting and classifying pollen, bringing together literature published from a wide spectrum of sources. We consider which attempts offer the most potential for an automated palynology system for universal application across all fields of research concerned with pollen classification and counting. We discuss what is required to make the datasets of these automated systems as acceptable as those produced by human palynologists, and present suggestions for how automation will generate novel approaches to counting and classifying pollen that have hitherto been unthinkable.