Measuring Biodiversity and Extinction-Present and Past

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?

Ancient plant DNA in lake sediments

Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 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.

Principles and methods for automated palynology

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.

Determining the response of African biota to climate change: using the past to model the future

Prediction of biotic responses to future climate change in tropical Africa tends to be based on two modelling approaches: bioclimatic species envelope models and dynamic vegetation models. Another complementary but underused approach is to examine biotic responses to similar climatic changes in the past as evidenced in fossil and historical records. This paper reviews these records and highlights the information that they provide in terms of understanding the local- and regional-scale responses of African vegetation to future climate change. A key point that emerges is that a move to warmer and wetter conditions in the past resulted in a large increase in biomass and a range distribution of woody plants up to 400–500 km north of its present location, the so-called greening of the Sahara. By contrast, a transition to warmer and drier conditions resulted in a reduction in woody vegetation in many regions and an increase in grass/savanna-dominated landscapes. The rapid rate of climate warming coming into the current interglacial resulted in a dramatic increase in community turnover, but there is little evidence for widespread extinctions. However, huge variation in biotic response in both space and time is apparent with, in some cases, totally different responses to the same climatic driver. This highlights the importance of local features such as soils, topography and also internal biotic factors in determining responses and resilience of the African biota to climate change, information that is difficult to obtain from modelling but is abundant in palaeoecological records.

Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia

Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.

Holocene pollen sequences as a record of competitive interactions among tree populations

The distributions of plant species in modern communities are often intensively studied in order to elucidate the basis of species richness and the maintenance of community structure. The Holocene pollen record provides an opportunity for an historical approach to the understanding of modern forest communities. Pollen data can provide evidence for the role of inter-specific competition in determining the composition of forest communities. The pollen data may point to those interactions where experiments to clarify the mechanisms of competition would be most relevant.

Phylogeographic insights into cryptic glacial refugia

The glacial episodes of the Quaternary (2.6 million years ago-present) were a major factor in shaping the present-day distributions of extant flora and fauna, with expansions and contractions of the ice sheets rendering large areas uninhabitable for most species. Fossil records suggest that many species survived glacial maxima by retreating to refugia, usually at lower latitudes. Recently, phylogeographic studies have given support to the existence of previously unknown, or cryptic, refugia. Here we summarise many of these insights into the glacial histories of species in cryptic refugia gained through phylogeographic approaches. Understanding such refugia might be important as the Earth heads into another period of climate change, in terms of predicting the effects on species distribution and survival.

Correction for Willis et al. , How can a knowledge of the past help to conserve the future? Biodiversity conservation and the relevance of long-term ecological studies

Correction for ‘How can a knowledge of the past help to conserve the future? Biodiversity conservation and the relevance of long-term ecological studies’ by Katherine J. Willis, Miguel B. Araújo, Keith D. Bennett, Blanca Figueroa-Rangel, Cynthia A. Froyd and Norman Myers (Phil. Trans. R. Soc. B 362 , 175–186. (doi: 10.1098/rstb.2006.1977 )).

The dates of the textual citations and the entries in the reference list for the following references should have been 2007 but were incorrectly given as 2006. The correct forms of these references are given below.

How can a knowledge of the past help to conserve the future? Biodiversity conservation and the relevance of long-term ecological studies

This paper evaluates how long-term records could and should be utilized in conservation policy and practice. Traditionally, there has been an extremely limited use of long-term ecological records (greater than 50 years) in biodiversity conservation. There are a number of reasons why such records tend to be discounted, including a perception of poor scale of resolution in both time and space, and the lack of accessibility of long temporal records to non-specialists. Probably more important, however, is the perception that even if suitable temporal records are available, their roles are purely descriptive, simply demonstrating what has occurred before in Earth's history, and are of little use in the actual practice of conservation. This paper asks why this is the case and whether there is a place for the temporal record in conservation management. Key conservation initiatives related to extinctions, identification of regions of greatest diversity/threat, climate change and biological invasions are addressed. Examples of how a temporal record can add information that is of direct practicable applicability to these issues are highlighted. These include (i) the identification of species at the end of their evolutionary lifespan and therefore most at risk from extinction, (ii) the setting of realistic goals and targets for conservation 'hotspots', and (iii) the identification of various management tools for the maintenance/restoration of a desired biological state. For climate change conservation strategies, the use of long-term ecological records in testing the predictive power of species envelope models is highlighted, along with the potential of fossil records to examine the impact of sea-level rise. It is also argued that a long-term perspective is essential for the management of biological invasions, not least in determining when an invasive is not an invasive. The paper concludes that often inclusion of a long-term ecological perspective can provide a more scientifically defensible basis for conservation decisions than the one based only on contemporary records. The pivotal issue of this paper is not whether long-term records are of interest to conservation biologists, but how they can actually be utilized in conservation practice and policy.

How can a knowledge of the past help to conserve the future? Biodiversity conservation and the relevance of long-term ecological studies

This paper evaluates how long-term records could and should be utilized in conservation policy and practice. Traditionally, there has been an extremely limited use of long-term ecological records (greater than 50 years) in biodiversity conservation. There are a number of reasons why such records tend to be discounted, including a perception of poor scale of resolution in both time and space, and the lack of accessibility of long temporal records to non-specialists. Probably more important, however, is the perception that even if suitable temporal records are available, their roles are purely descriptive, simply demonstrating what has occurred before in Earth's history, and are of little use in the actual practice of conservation. This paper asks why this is the case and whether there is a place for the temporal record in conservation management. Key conservation initiatives related to extinctions, identification of regions of greatest diversity/threat, climate change and biological invasions are addressed. Examples of how a temporal record can add information that is of direct practicable applicability to these issues are highlighted. These include (i) the identification of species at the end of their evolutionary lifespan and therefore most at risk from extinction, (ii) the setting of realistic goals and targets for conservation 'hotspots', and (iii) the identification of various management tools for the maintenance/restoration of a desired biological state. For climate change conservation strategies, the use of long-term ecological records in testing the predictive power of species envelope models is highlighted, along with the potential of fossil records to examine the impact of sea-level rise. It is also argued that a long-term perspective is essential for the management of biological invasions, not least in determining when an invasive is not an invasive. The paper concludes that often inclusion of a long-term ecological perspective can provide a more scientifically defensible basis for conservation decisions than the one based only on contemporary records. The pivotal issue of this paper is not whether long-term records are of interest to conservation biologists, but how they can actually be utilized in conservation practice and policy.

Ancient DNA from pollen: a genetic record of population history in Scots pine

Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100-year old and 10 000-year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.

Continuing the debate on the role of Quaternary environmental change for macroevolution

The Quaternary has been a period of dramatic environmental change for the past 1.8 Myr, with major shifts in distributions and abundances of terrestrial and marine organisms. The evolutionary consequences of this have been debated since the nineteenth century. However, the lack of accurate relative and absolute time-scales for evolutions and environmental change inhibited progress. We do now have an understanding of time-scales. Palaeoecology has demonstrated the individualistic nature of species' response to environmental change, but lacks a means of determining ancestry. DNA characterization of modern populations in relation to their distributions nicely complements palaeoecological results by contributing ancestry. The chance to understand how species originate and the causal factors of speciation (environmental change or otherwise) may be within reach.

The last glacial-Holocene transition in southern Chile

Warming at the last glacial termination in the North Atlantic region was interrupted by a period of renewed glacial activity during the Younger Dryas chronozone (YDC). The underlying mechanism of this cooling remains elusive, but hypotheses turn on whether it was a global or a North Atlantic phenomenon. Chronological, sedimentological, and palaeoecological records from sediments of small lakes in oceanic southern Chile demonstrate that there was no YDC cooling in southern Chile. It is therefore likely that there was little or no cooling in southern Pacific surface waters and hence that YDC cooling in the North Atlantic was a regional, rather than global, phenomenon.

Radionuclides in deer and elk from Los Alamos National Laboratory and the doses to humans from the ingestion of muscle and bone

This paper summarizes radionuclide concentrations (3H, 90Sr, 137Cs, 238Pu, 239,240Pu, 241Am, and totU) in muscle and bone tissue of mule deer (Odocoileus hemionus) and Rocky Mountain elk (Cervus elaphus) collected from Los Alamos National Laboratory (LANL), Los Alamos, New Mexico, lands from 1991 through 1998. Also, the committed effective dose equivalent (CEDE) and the risk of excess cancer fatalities (RECF) to people who ingest muscle and bone from deer and elk collected from LANL lands were estimated. Most radionuclide concentrations in muscle and bone from individual deer (n = 11) and elk (n = 22) collected from LANL lands were either at less than detectable quantities (where the analytical result was smaller than two counting uncertainties) and/or within upper (95%) level background (BG) concentrations. As a group, most radionuclides in muscle and bone of deer and elk from LANL lands were not significantly higher (p < 0.10) than in similar tissues from deer (n = 3) and elk (n = 7) collected from BG locations. Also, elk that had been radio collared and tracked for two years and spent an average time of 50% of LANL lands were not significantly different in most radionuclides from road kill elk that have been collected as part of the environmental surveillance program. Overall, the upper (95%) level net CEDEs (the CEDE plus two sigma for each radioisotope minus background) at the most conservative ingestion rate (50 lbs of muscle and 13 lbs of bone) were as follows: deer muscle = 0.22 mrem y-1 (2.2 microSv y-1), deer bone = 3.8 mrem y-1 (38 microSv y-1), elk muscle = 0.12 mrem y-1 (1.2 microSv y-1), and elk bone = 1.7 mrem y-1 (17 microSv y-1). All CEDEs were far below the International Commission on Radiological Protection guideline of 100 mrem y-1 (1000 microSv y-1), and the highest muscle plus bone net CEDE corresponded to a RECF of 2E-06, which is far below the Environmental Protection Agency upper level guideline of 1E-04.

Determination of the number of zones in a biostratigraphical sequence

Current methods for numerical zonation of biostratigraphic sequences neither assess the reliability of zones identified nor provide any means of determining the number of zones that are 'significant' (based on structure in the data set, rather than the stochastic element). These problems can be overcome by using the broken-stick model to assess the significance of zones against a model of random distribution of zones within a sequence. The broken-stick model is described and its application demonstrated on actual data sets. Additionally, simulation modelling is used to assess the uncertainty of the location of individual zone markers, given the errors of the original data. These widely-applicable methods make it possible to identify zones rigorously and consistently. The potential in biostratigraphy and correlation includes the recognition, correlation and subdivision of chronostratipraphic units in long Quaternary sequences.

Pollen analysis of a Quaternary peat sequence on Gough Island, South Atlantic

A peat sequence on Gough Island, South Atlantic, is described. The deposit is at least 43 000 years old, and may be early Quaternary in age. Pollen analyses suggest a flora and vegetation on Cough Island similar to those of today, supporting conclusions based on pre-Holocene pollen samples from islands in the Tristan da Cunha group. The present flora has probably been on Cough Island continuously for at least the last 40000 years, and is not a Holocene immigrant flora.

Age related differences in binding of concanavalin A to plasma membranes of isolated neurons

Neurons isolated from the lateral vestibular nucleus of young adult and senescent Fischer-344 rats were incubated with fluorescamine-labelled Concanavalin A (fl-Con A) alone, or following incubation in trypsin or Vibrio cholerae neuraminidase. They were then observed and photographed. Microdensitometric analysis of fluorescence micrographs showed that senescent rat neurons were significantly more fluorescent than those from young adult rats. Additionally, either patches or caps of fl-Con A were seen on the surface of neurons from senescent rats, while most young adult rat neurons bound fl-Con A uniformly. Pretreatment with trypsin or neuraminidase had no effect on the amount of fluorescence on the surface of senescent rat neurons, and only a slight effect on the surface distribution. Trypsin and neuronal plasma membranes of young adult rats and a rearrangement of the binding pattern in the majority of neurons observed.