bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein trafficking on sliding clamps
Authors: López de Saro Francisco , Georgescu Roxana E. , Leu Frank , O'Donnell Mike
Published: April 2004

The sliding clamps of chromosomal replicases are acted upon by both the clamp loader and DNA polymerase. Several other proteins and polymerases also interact with the clamp. These proteins bind the clamp at the same spot and use it in sequential fashion. First the clamp loader must bind the clamp in order to load it onto DNA, but directly thereafter the clamp loader must clear away from the clamp so it can be used by the replicative DNA polymerase. At the end of replication, the replicase is ejected from the clamp, which presumably allows the clamp to interact with yet other proteins after its use by the replicase. This paper describes how different proteins in the
Escherichia coli
replicase, DNA polymerase III holoenzyme, coordinate their traffic flow on the clamp. The mechanism by which traffic flow on the β; clamp is directed is based on competition of the proteins for the clamp, where DNA structure modulates the competition. It seems likely that the principles will generalize to a traffic flow of other factors on these circular clamp proteins.
Disentangling DNA during replication: a tale of two strands
Authors: Hardy Christine D. , Crisona Nancy J. , Stone Michael D. , Cozzarelli Nicholas R.
Published: April 2004

The seminal papers by Watson and Crick in 1953 on the structure and function of DNA clearly enunciated the challenge their model presented of how the intertwined strands of DNA are unwound and separated for replication to occur. We first give a historical overview of the major discoveries in the past 50 years that address this challenge. We then describe in more detail the cellular mechanisms responsible for the unlinking of DNA. No single strategy on its own accounts for the complete unlinking of chromosomes required for DNA segregation to proceed. Rather, it is the combined effects of topoisomerase action, chromosome organization and DNA–condensing proteins that allow the successful partitioning of chromosomes into dividing cells. Finally, we propose a model of chromosome structure, consistent with recent findings, that explains how the problem of unlinking is alleviated by the division of chromosomal DNA into manageably sized domains.
Recombination and chromosome segregation
Authors: Sherratt David J. , Søballe Britta , Barre François–Xavier , Filipe Sergio , Lau Ivy , Massey Thomas , Yates James
Published: April 2004

The duplication of DNA and faithful segregation of newly replicated chromosomes at cell division is frequently dependent on recombinational processes. The rebuilding of broken or stalled replication forks is universally dependent on homologous recombination proteins. In bacteria with circular chromosomes, crossing over by homologous recombination can generate dimeric chromosomes, which cannot be segregated to daughter cells unless they are converted to monomers before cell division by the conserved Xer site–specific recombination system. Dimer resolution also requires FtsK, a division septum–located protein, which coordinates chromosome segregation with cell division, and uses the energy of ATP hydrolysis to activate the dimer resolution reaction. FtsK can also translocate DNA, facilitate synapsis of sister chromosomes and minimize entanglement and catenation of newly replicated sister chromosomes. The visualization of the replication/recombination–associated proteins, RecQ and RarA, and specific genes within livingEscherichia colicells, reveals further aspects of the processes that link replication with recombination, chromosome segregation and cell division, and provides new insight into how these may be coordinated.
Mechanisms of replication fork restart inEscherichia coli
Authors: Marians Kenneth J.
Published: April 2004

Replication of the genome is crucial for the accurate transmission of genetic information. It has become clear over the last decade that the orderly progression of replication forks in both prokaryotes and eukaryotes is disrupted with high frequency by encounters with various obstacles either on or in the template strands. Survival of the organism then becomes dependent on both removal of the obstruction and resumption of replication. This latter point is particularly important in bacteria, where the number of replication forks per genome is nominally only two. Replication restart inEscherichia coliis accomplished by the action of the restart primosomal proteins, which use both recombination intermediates and stalled replication forks as substrates for loading new replication forks. These reactions have been reconstituted with purified recombination and replication proteins.
Repairing a double–strand chromosome break by homologous recombination: revisiting Robin Holliday's model
Authors: Haber James E. , Ira Gregorz , Malkova Anna , Sugawara Neal
Published: April 2004

Since the pioneering model for homologous recombination proposed by Robin Holliday in 1964, there has been great progress in understanding how recombination occurs at a molecular level. In the budding yeastSaccharomyces cerevisiae, one can follow recombination by physically monitoring DNA after the synchronous induction of a double–strand break (DSB) in both wild–type and mutant cells. A particularly well–studied system has been the switching of yeast mating–type (MAT) genes, where a DSB can be induced synchronously by expression of the site–specific HO endonuclease. Similar studies can be performed in meiotic cells, where DSBs are created by the Spo11 nuclease. There appear to be at least two competing mechanisms of homologous recombination: a synthesis–dependent strand annealing pathway leading to noncrossovers and a two–end strand invasion mechanism leading to formation and resolution of Holliday junctions (HJs), leading to crossovers. The establishment of a modified replication fork during DSB repair links gene conversion to another important repair process, break–induced replication. Despite recent revelations, almost 40 years after Holliday's model was published, the essential ideas he proposed of strand invasion and heteroduplex DNA formation, the formation and resolution of HJs, and mismatch repair, remain the basis of our thinking.
RAD51 localization and activation following DNA damage
Authors: Tarsounas Madalena , Davies Adelina A. , West Stephen C.
Published: April 2004

The efficient repair of double–strand breaks in DNA is critical for the maintenance of genome stability. In response to ionizing radiation and other DNA–damaging agents, the RAD51 protein, which is essential for homologous recombination, relocalizes within the nucleus to form distinct foci that can be visualized by microscopy and are thought to represent sites where repair reactions take place. The formation of RAD51 foci in response to DNA damage is dependent upon BRCA2 and a series of proteins known as the RAD51 paralogues (RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3), indicating that the components present within foci assemble in a carefully orchestrated and ordered manner. By contrast, RAD51 foci that form spontaneously as cells undergo DNA replication at S phase occur without the need for BRCA2 or the RAD51 paralogues. It is known that BRCA2 interacts directly with RAD51 through a series of degenerative motifs known as the BRC repeats. These interactions modulate the ability of RAD51 to bind DNA. Taken together, these observations indicate that BRCA2 plays a critical role in controlling the actions of RAD51 at both the microscopic (focus formation) and molecular (DNA binding) level.
Meiotic recombination hot spots and human DNA diversity
Authors: Jeffreys Alec J. , Holloway J. Kim , Kauppi Liisa , May Celia A. , Neumann Rita , Slingsby M. Timothy , Webb Adam J.
Published: April 2004

Meiotic recombination plays a key role in the maintenance of sequence diversity in the human genome. However, little is known about the fine–scale distribution and processes of recombination in human chromosomes, or how these impact on patterns of human diversity. We have therefore developed sperm typing systems that allow human recombination to be analysed at very high resolution. The emerging picture is that human crossovers are far from randomly distributed but instead are targeted into very narrow hot spots that can profoundly influence patterns of haplotype diversity in the human genome. These hot spots provide fundamental information on processes of human crossover and gene conversion, as well as evidence that they can violate basic rules of Mendelian inheritance.
Perspectives
Authors: Brenner Sydney
Published: April 2004

Perspectives
Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases
Authors: Steitz Thomas A. , Yin Y. Whitney
Published: April 2004

The structures of DNA polymerases from different families show common features and significant differences that shed light on the ability of these enzymes to accurately copy DNA and translocate. The structure of a B family DNA polymerase from phage RB69 exhibits an active–site closing conformational change in the fingers domain upon forming a ternary complex with primer template in deoxynucleoside triphosphate. The rotation of the fingers domain α–helices by 60° upon dNTP binding is analogous to the changes seen in other families of polymerases. When the 3' terminus is bound to the editing 3' exonuclease active site, the orientation of the DNA helix axis changes by 40° and the thumb domain re–orients with the DNA. Structures of substrate and product complexes of T7 RNA polymerase, a structural homologue of T7 DNA polymerase, show that family polymerases use the rotation conformational change of the fingers domain to translocate down the DNA. The fingers opening rotation that results in translocation is powered by the release of the product pyrophosphate and also enables the Pol I family polymerases to function as a helicase in displacing the downstream non–template strand from the template strand.
Current issues in the utility of
19
F nuclear magnetic resonance methodologies for the assessment of tumour hypoxia
Authors: Robinson Simon P. , Griffiths John R.
Published: April 2004

It is now well established that uncontrolled proliferation of tumour cells together with the chaotic and poorly regulated blood supply of solid tumours result in tissue hypoxia, and that hypoxic regions of tumours are resistant to radiotherapy and chemotherapy. The development and application of non–invasive methods to rapidly determine the degree and extent of tumour hypoxia in an individual tumour would clearly enhance cancer treatment strategies. This review describes the current status of two
19
F nuclear magnetic resonance (NMR) methodologies that have been exploited to investigate tumour hypoxia, namely: (i)
19
F NMR oximetry following administration of perfluorocarbons, from which tumour
p
O
2
measurements can be made; and (ii)
19
F NMR measurements of the tumour retention of fluorinated 2–nitroimidazoles.
The role of Quaternary environmental change in plant macroevolution: the exception or the rule?
Authors: Willis Katherine J. , Niklas Karl J.
Published: April 2004

The Quaternary has been described as an important time for genetic diversification and speciation. This is based on the premise that Quaternary climatic conditions fostered the isolation of populations and, in some instances, allopatric speciation. However, the ‘Quaternary Ice–Age speciation model’ rests on two key assumptions: (i) that biotic responses to climate change during the Quaternary were significantly different from those of other periods in Earth's history; and (ii) that the mechanisms of isolation during the Quaternary were sufficient in time and space for genetic diversification to foster speciation. These assumptions are addressed by examining the plant fossil record for the Quaternary (in detail) and for the past 410 Myr, which encompasses previous intervals of icehouse Earth. Our examination of the Quaternary record indicates that floristic responses to climate changes during the past 1.8 Myr were complex and that a distinction has to be made between those plants that were able to withstand the extremes of glacial conditions and those that could not. Generation times are also important as are different growth forms (e.g. herbaceous annuals and arborescent perennials), resulting in different responses in terms of genetic divergence rates during isolation. Because of these variations in the duration of isolation of populations and genomic diversification rates, no canonical statement about the predominant floristic response to climatic changes during the Quaternary (i.e. elevated rates of speciation or extinction, or stasis) is currently possible. This is especially true because of a sampling bias in terms of the fossil record of tree species over that of species with non–arborescent growth forms. Nevertheless, based on the available information, it appears that the dominant response of arborescent species during the Quaternary was extinction rather than speciation or stasis. By contrast, our examination of the fossil record of vascular plants for the past 410 Myr indicates that speciation rates often increased during long intervals of icehouse Earth (spanning up to 50 Myr). Therefore, longer periods of icehouse Earth than those occurring during the Quaternary may have isolated plant populations for sufficiently long periods of time to foster genomic diversification and allopatric speciation. Our results highlight the need for more detailed study of the fossil record in terms of finer temporal and spatial resolution than is currently available to examine the significance of intervals of icehouse Earth. It is equally clear that additional and detailed molecular studies of extant populations of Quaternary species are required in order to determine the extent to which these ‘relic’ species have genomically diversified across their current populations.
Genetic consequences of climatic oscillations in the Quaternary
Authors: Hewitt G. M.
Published: April 2004

An appreciation of the scale and frequency of climatic oscillations in the past few million years is modifying our views on how evolution proceeds. Such major events caused extinction and repeated changes in the ranges of those taxa that survived. Their spatial effects depend on latitude and topography, with extensive extinction and recolonization in higher latitudes and altitudinal shifts and complex refugia nearer the tropics. The associated population dynamics varied with life history and geography, and the present genetic constitution of the populations and species carry attenuated signals of these past dynamics. Phylogeographic studies with DNA have burgeoned recently and studies are reviewed from the arctic, temperate and tropical regions, seeking commonalities of cause in the resulting genetic patterns. Arctic species show distinct shallow genetic clades with common geographical boundaries. Thus Beringia is distinct phylogeographically, but its role as a refugial source is complex. Arctic taxa do not show the common genetic pattern of southern richness and northern purity in north-temperate species. Temperate refugial regions in Europe and North America show relatively deep DNA divergence for many taxa, indicating their presence over several Ice Ages, and suggesting a mode of speciation by repeated allopatry. DNA evidence indicates temperate species in Europe had different patterns of postglacial colonization across the same area and different ones in previous oscillations, whereas the northwest region of North America was colonized from the north, east and south. Tropical montane regions contain deeply diverged lineages, often in a relatively small geographical area, suggesting their survival there from the Pliocene. Our poor understanding of refugial biodiversity would benefit from further combined fossil and genetic studies.
Impact of Ice Ages on the genetic structure of trees and shrubs
Authors: Lascoux Martin , Palmé Anna E. , Cheddadi Rachid , Latta Robert G.
Published: April 2004

Data on the genetic structure of tree and shrub populations on the continental scale have accumulated dramatically over the past decade. However, our ability to make inferences on the impact of the last ice age still depends crucially on the availability of informative palaeoecological data. This is well illustrated by the results from a recent project, during which new pollen fossil maps were established and the variation in chloroplast DNA was studied in 22 European species of trees and shrubs. Species exhibit very different levels of genetic variation between and within populations, and obviously went through very different histories after Ice Ages. However, when palaeoecological data are non-informative, inferences on past history are difficult to draw from entirely genetic data. On the other hand, as illustrated by a study in ponderosa pine, when we can infer the species' history with some certainty, coalescent simulations can be used and new hypotheses can be tested.
Glacial refugia and reticulate evolution: the case of the Tasmanian eucalypts
Authors: McKinnon Gay E. , Jordan Gregory J. , Vaillancourt René E. , Steane Dorothy A. , Potts Brad M.
Published: April 2004

Tasmania is a natural laboratory for investigating the evolutionary processes of the Quaternary. It is a large island lying 40–44° S, which was repeatedly glaciated and linked to southeastern continental Australia during the Quaternary. Climate change promoted both the isolation of species in glacial refugia, and an exchange between Tasmanian and mainland floras.Eucalyptusis a complex and diverse genus, which has increased in abundance in Australia over the past 100 kyr, probably in response to higher fire frequency. Morphological evidence suggests that gene flow may have occurred between many eucalypt species after changes in their distribution during the Quaternary. This paper summarizes recent genetic evidence for migration and introgressive hybridization in TasmanianEucalyptus. Maternally inherited chloroplast DNA reveals a long–term persistence of eucalypts in southeastern Tasmanian refugia, coupled with introgressive hybridization involving many species. Detailed analysis of the widespread speciesEucalyptus globulussuggests that migration from mainland Australia was followed by introgression involving a rare Tasmanian endemic. The data support the hypothesis that changes in distribution of interfertile species during the Quaternary have promoted reticulate evolution inEucalyptus.
Several million years of stability among insect species because of, or in spite of, Ice Age climatic instability?
Authors: Coope G. R.
Published: April 2004

There is a curious paradox in the evolutionary legacy of Ice Ages. Studies of modern species suggest that they are currently evolving in response to changing environments. If extrapolated into the context of Quaternary Ice Ages, this evidence would suggest that the frequent climatic changes should have stimulated the evolutionary process and thus increased the rates of change within species and the number of speciation events. Extinction rates would, similarly, be high. Quaternary insect studies call into question these interpretations. They indicate that insect species show a remarkable degree of stability throughout the Ice Age climatic oscillations. The paradox arises from the apparent contradiction between abundant evidence of incipient speciation in insect populations at the present day and the evidence that, in the geological past, this apparently did not lead to sustained evolution.
Ice Ages and the mitochondrial DNA chronology of human dispersals: a review
Authors: Forster Peter
Published: April 2004

Modern DNA, in particular maternally inherited mitochondrial DNA (mtDNA), is now routinely used to trace ancient human migration routes and to obtain absolute dates for genetic prehistory. The errors on absolute genetic dates are often large (50% or more) and depend partly on the inherent evolutionary signal in the DNA data, and partly on our imperfect knowledge of the DNA mutation rate. Despite their imprecision, the genetic dates do provide an independent, consistent and global chronology linking living humans with their ancestors. Combining this chronology with archaeological and climatological data, most of our own mtDNA studies during the past decade strongly imply a major role for palaeoclimate in determining conditions for prehistoric migrations and demographic expansions. This paper summarizes our interpretation of the genetic findings, covering the initial and modest spread of humans within Africa more than 100 ka, the striking re–expansion within Africa 60–80 ka, leading ultimately to the out–of–Africa migration of a single, small group which settled in Australia, Eurasia and America during windows of opportunity at least partly dictated by fluctuations in sea–levels and climatic conditions.
Continuing the debate on the role of Quaternary environmental change for macroevolution
Authors: Bennett K. D.
Published: April 2004

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.
Introduction
Authors: Sherratt David , West Stephen
Published: April 2004

Introduction
From a single double helix to paired double helices and back
Authors: Nasmyth Kim , Schleiffer Alexander
Published: April 2004

The propagation of our genomes during cell proliferation depends on the movement of sister DNA molecules produced by DNA replication to opposite sides of the cell before it divides. This feat is achieved by microtubules in eukaryotic cells but it has long remained a mystery how cells ensure that sister DNAs attach to microtubules with opposite orientations, known as amphitelic attachment. It is currently thought that sister chromatid cohesion has a crucial role. By resisting the forces exerted by microtubules, sister chromatid cohesion gives rise to tension that is thought essential for stabilizing kinetochore–microtubule attachments. Efficient amphitelic attachment is therefore achieved by an error correction mechanism that selectively eliminates connections that do not give rise to tension. Cohesion between sister chromatids is mediated by a multisubunit complex called cohesin which forms a gigantic ring structure. It has been proposed that sister DNAs are held together owing to their becoming entrapped within a single cohesin ring. Cohesion between sister chromatids is destroyed at the metaphase to anaphase transition by proteolytic cleavage of cohesin's Scc1 subunit by a thiol protease called separase, which severs the ring and thereby releases sister DNAs.
Hypervariability, suppressed recombination and the genetics of individuality
Authors: Olson M. V. , Kas A. , Bubb K. , Qui R. , Smith E. E. , Raymond C. K. , Kaul R.
Published: April 2004

We define ‘genetic individuality’ as intraspecies variation that has substantial heritability and involves traits that are sufficiently common that they can be observed in any modest–sized sampling of individuals. We propose that genetic individuality is largely shaped by the combinatory shuffling of a modest number of genes, each of which exists as a family of functionally and structurally diverged alleles. Unequivocal examples of such allele families are found at the O–antigen–biosynthetic locus inPseudomonas aeruginosaand the human leucocyte antigen locus in humans. We examine characteristic features of these allele families and explore the possibility that genetic loci with similar characteristics can be recognized in a whole–genome scan of human genetic variation.
Introduction
Authors: Willis K. J. , Bennett K. D. , Walker D.
Published: April 2004

Introduction
Increasing biomass in Amazonian forest plots
Authors: Baker Timothy R. , Phillips Oliver L. , Malhi Yadvinder , Almeida Samuel , Arroyo Luzmila , Di Fiore Anthony , Erwin Terry , Higuchi Niro , Killeen Timothy J. , Laurance Susan G. , Laurance William F. , Lewis Simon L. , Monteagudo Abel , Neill David A. , Núñez Vargas Percy , Pitman Nigel C. A. , Silva J. Natalino M. , Vásquez Martínez Rodolfo
Published: April 2004

A previous study by Phillips
et al
. of changes in the biomass of permanent sample plots in Amazonian forests was used to infer the presence of a regional carbon sink. However, these results generated a vigorous debate about sampling and methodological issues. Therefore we present a new analysis of biomass change in old–growth Amazonian forest plots using updated inventory data. We find that across 59 sites, the above–ground dry biomass in trees that are more than 10 cm in diameter (AGB) has increased since plot establishment by 1.22 ± 0.43 Mg per hectare per year (ha
−1
yr
−1
), where 1 ha = 10
4
m
2
), or 0.98 ± 0.38 Mg ha
−1
yr
−1
if individual plot values are weighted by the number of hectare years of monitoring. This significant increase is neither confounded by spatial or temporal variation in wood specific gravity, nor dependent on the allometric equation used to estimate AGB. The conclusion is also robust to uncertainty about diameter measurements for problematic trees: for 34 plots in western Amazon forests a significant increase in AGB is found even with a conservative assumption of zero growth for all trees where diameter measurements were made using optical methods and/or growth rates needed to be estimated following fieldwork. Overall, our results suggest a slightly greater rate of net stand–level change than was reported by Phillips
et al
. Considering the spatial and temporal scale of sampling and associated studies showing increases in forest growth and stem turnover, the results presented here suggest that the total biomass of these plots has on average increased and that there has been a regional–scale carbon sink in old–growth Amazonian forests during the previous two decades.
Ecological responses to El Niño–induced surface fires in central Brazilian Amazonia: management implications for flammable tropical forests
Authors: Barlow Jos , Peres Carlos A.
Published: April 2004

Over the past 20 years the combined effects of El Niño–induced droughts and land–use change have dramatically increased the frequency of fire in humid tropical forests. Despite the potential for rapid ecosystem alteration and the current prevalence of wildfire disturbance, the consequences of such fires for tropical forest biodiversity remain poorly understood. We provide a pan–tropical review of the current state of knowledge of these fires, and include data from a study in a seasonally dry
terra firme
forest of central Brazilian Amazonia. Overall, this study supports predictions that rates of tree mortality and changes in forest structure are strongly linked to burn severity. The potential consequences for biomass loss and carbon emissions are explored. Despite the paucity of data on faunal responses to tropical forest fires, some trends are becoming apparent; for example, large canopy frugivores and understorey insectivorous birds appear to be highly sensitive to changes in forest structure and composition during the first 3 years after fires. Finally, we appraise the management implications of fires and evaluate the viability of techniques and legislation that can be used to reduce forest flammability, prevent anthropogenic ignition sources from coming into contact with flammable forests and aid the post–fire recovery process.
Error propagation and scaling for tropical forest biomass estimates
Authors: Chave Jerome , Condit Richard , Aguilar Salomon , Hernandez Andres , Lao Suzanne , Perez Rolando
Published: April 2004

The above-ground biomass (AGB) of tropical forests is a crucial variable for ecologists, biogeochemists, foresters and policymakers. Tree inventories are an efficient way of assessing forest carbon stocks and emissions to the atmosphere during deforestation. To make correct inferences about long-term changes in biomass stocks, it is essential to know the uncertainty associated with AGB estimates, yet this uncertainty is rarely evaluated carefully. Here, we quantify four types of uncertainty that could lead to statistical error in AGB estimates: (i) error due to tree measurement; (ii) error due to the choice of an allometric model relating AGB to other tree dimensions; (iii) sampling uncertainty, related to the size of the study plot; (iv) representativeness of a network of small plots across a vast forest landscape. In previous studies, these sources of error were reported but rarely integrated into a consistent framework. We estimate all four terms in a 50 hectare (ha, where 1 ha = 104 m2) plot on Barro Colorado Island, Panama, and in a network of 1 ha plots scattered across central Panama. We find that the most important source of error is currently related to the choice of the allometric model. More work should be devoted to improving the predictive power of allometric models for biomass.
Sources or sinks? The responses of tropical forests to current and future climate and atmospheric composition
Authors: Clark Deborah A.
Published: April 2004

How tropical rainforests are responding to the ongoing global changes in atmospheric composition and climate is little studied and poorly understood. Although rising atmospheric carbon dioxide (CO2) could enhance forest productivity, increased temperatures and drought are likely to diminish it. The limited field data have produced conflicting views of the net impacts of these changes so far. One set of studies has seemed to point to enhanced carbon uptake; however, questions have arisen about these findings, and recent experiments with tropical forest trees indicate carbon saturation of canopy leaves and no biomass increase under enhanced CO2. Other field observations indicate decreased forest productivity and increased tree mortality in recent years of peak temperatures and drought (strong El Niño episodes). To determine current climatic responses of forests around the world tropics will require careful annual monitoring of ecosystem performance in representative forests. To develop the necessary process–level understanding of these responses will require intensified experimentation at the whole–tree and stand levels. Finally, a more complete understanding of tropical rainforest carbon cycling is needed for determining whether these ecosystems are carbon sinks or sources now, and how this status might change during the next century.
Contrasting simulated past and future responses of the Amazonian forest to atmospheric change
Authors: Cowling Sharon A. , Betts Richard A. , Cox Peter M. , Ettwein Virginia J. , Jones Chris D. , Maslin Mark A. , Spall Steven A.
Published: April 2004

Modelling simulations of palaeoclimate and past vegetation form and function can contribute to global change research by constraining predictions of potential earth system responses to future warming, and by providing useful insights into the ecophysiological tolerances and threshold responses of plants to varying degrees of atmospheric change. We contrasted HadCM3LC simulations of Amazonian forest at the last glacial maximum (LGM; 21 kyr ago) and a Younger Dryas–like period (13–12 kyr ago) with predicted responses of future warming to provide estimates of the climatic limits under which the Amazon forest remains relatively stable. Our simulations indicate that despite lower atmospheric CO2concentrations and increased aridity during the LGM, Amazonia remains mostly forested, and that the cooling climate of the Younger Dryas–like period in fact causes a trend towardincreasedabove–ground carbon balance relative to today. The vegetation feedbacks responsible for maintaining forest integrity in past climates (i.e. decreased evapotranspiration and reduced plant respiration) cannot be maintained into the future. Although elevated atmospheric CO2contributes to a positive enhancement of plant carbon and water balance, decreased stomatal conductance and increased plant and soil respiration cause a positive feedback that amplifies localized drying and climate warming. We speculate that the Amazonian forest is currently near its critical resiliency threshold, and that even minor climate warming may be sufficient to promote deleterious feedbacks on forest integrity.
Tropical forests and the global carbon cycle: impacts of atmospheric carbon dioxide, climate change and rate of deforestation
Authors: Cramer Wolfgang , Bondeau Alberte , Schaphoff Sibyll , Lucht Wolfgang , Smith Benjamin , Sitch Stephen
Published: April 2004

The remaining carbon stocks in wet tropical forests are currently at risk because of anthropogenic deforestation, but also because of the possibility of release driven by climate change. To identify the relative roles of CO
2
increase, changing temperature and rainfall, and deforestation in the future, and the magnitude of their impact on atmospheric CO
2
concentrations, we have applied a dynamic global vegetation model, using multiple scenarios of tropical deforestation (extrapolated from two estimates of current rates) and multiple scenarios of changing climate (derived from four independent offline general circulation model simulations). Results show that deforestation will probably produce large losses of carbon, despite the uncertainty about the deforestation rates. Some climate models produce additional large fluxes due to increased drought stress caused by rising temperature and decreasing rainfall. One climate model, however, produces an additional carbon sink. Taken together, our estimates of additional carbon emissions during the twenty–first century, for all climate and deforestation scenarios, range from 101 to 367 Gt C, resulting in CO
2
concentration increases above background values between 29 and 129 p.p.m. An evaluation of the method indicates that better estimates of tropical carbon sources and sinks require improved assessments of current and future deforestation, and more consistent precipitation scenarios from climate models. Notwithstanding the uncertainties, continued tropical deforestation will most certainly play a very large role in the build–up of future greenhouse gas concentrations.
Concerted changes in tropical forest structure and dynamics: evidence from 50 South American long-term plots
Authors: Lewis S. L. , Phillips O. L. , Baker T. R. , Lloyd J. , Malhi Y. , Almeida S. , Higuchi N. , Laurance W. F. , Neill D. A. , Silva J. N. M. , Terborgh J. , Torres Lezama A. , Vásquez Martinez R. , Brown S. , Chave J. , Kuebler C. , Núñez Vargas P. , Vinceti B.
Published: April 2004

Several widespread changes in the ecology of old–growth tropical forests have recently been documented for the late twentieth century, in particular an increase in stem turnover (pan–tropical), and an increase in above–ground biomass (neotropical). Whether these changes are synchronous and whether changes in growth are also occurring is not known. We analysed stand–level changes within 50 long–term monitoring plots from across South America spanning 1971–2002. We show that: (i) basal area (BA: sum of the cross–sectional areas of all trees in a plot) increased significantly over time (by

0.10 ±; 0.04

m
2
ha
−1
yr
−1
, mean ± 95%CI) as did both (ii) stand–level BA growth rates (sum of the increments of BA of surviving trees and BA of new trees that recruited into a plot); and (iii) stand–level BA mortality rates (sum of the cross–sectional areas of all trees that died in a plot). Similar patterns were observed on a per–stem basis: (i) stem density (number of stems per hectare; 1 hectare is 10
4
m
2
) increased significantly over time (

0.94 ± 0.63

stems ha
−1
yr
−1
); as did both (ii) stem recruitment rates; and (iii) stem mortality rates. In relative terms, the pools of BA and stem density increased by

0.38 ± 0.15%

and

0.18 ± 0.12%

yr
−1
, respectively. The fluxes into and out of these pools—stand–level BA growth, stand–level BA mortality, stem recruitment and stem mortality rates—increased, in relative terms, by an order of magnitude more. The gain terms (BA growth, stem recruitment) consistently exceeded the loss terms (BA loss, stem mortality) throughout the period, suggesting that whatever process is driving these changes was already acting before the plot network was established. Large long–term increases in stand–level BA growth and simultaneous increases in stand BA and stem density imply a continent–wide increase in resource availability which is increasing net primary productivity and altering forest dynamics. Continent–wide changes in incoming solar radiation, and increases in atmospheric concentrations of CO
2
and air temperatures may have increased resource supply over recent decades, thus causing accelerated growth and increased dynamism across the world's largest tract of tropical forest.
Responses of Amazonian ecosystems to climatic and atmospheric carbon dioxide changes since the last glacial maximum
Authors: Mayle Francis E. , Beerling David J. , Gosling William D. , Bush Mark B.
Published: April 2004

The aims of this paper are to review previously published palaeovegetation and independent palaeoclimatic datasets together with new results we present from dynamic vegetation model simulations and modern pollen rain studies to: (i) determine the responses of Amazonian ecosystems to changes in temperature, precipitation and atmospheric CO2concentrations that occurred since the Last Glacial Maximum (LGM),ca. 21 000 years ago; and (ii) use this long–term perspective to predict the likely vegetation responses to future climate change. Amazonia remained predominantly forested at the LGM, although the combination of reduced temperatures, precipitation and atmospheric CO2concentrations resulted in forests structurally and floristically quite different from those of today. Cold–adapted Andean taxa mixed with rainforest taxa in central areas, while dry forest species and lianas probably became important in the more seasonal southern Amazon forests and savannahs expanded at forest–savannah ecotones. Net primary productivity (NPP) and canopy density were significantly lower than today. Evergreen rainforest distribution and NPP increased during the glacial—Holocene transition owing to ameliorating climatic and CO2conditions. However, reduced precipitation in the Early–Mid–Holocene (ca. 8000–3600 years ago) caused widespread, frequent fires in seasonal southern Amazonia, causing increased abundance of drought–tolerant dry forest taxa and savannahs in ecotonal areas. Rainforests expanded once more in the Late Holocene owing to increased precipitation caused by greater austral summer insolation, although some of this forest expansion (e.g. in parts of the Bolivian Beni) is clearly caused by palaeo Indian landscape modification. The plant communities that existed during the Early–Mid–Holocene may provide insights into the kinds of vegetation response expected from similar increases in temperature and aridity predicted for the twenty–first century. We infer that ecotonal areas near the margins of the Amazon Basin are liable to be most sensitive to future environmental change and should therefore be targeted with conservation strategies that allow ‘natural’ species movements and plant community re–assortments to occur.
Historical climate change and speciation: neotropical seasonally dry forest plants show patterns of both Tertiary and Quaternary diversification
Authors: Pennington R. Toby , Lavin Matt , Prado Darién E. , Pendry Colin A. , Pell Susan K. , Butterworth Charles A.
Published: April 2004

Historical climate changes have had a major effect on the distribution and evolution of plant species in the neotropics. What is more controversial is whether relatively recent Pleistocene climatic changes have driven speciation, or whether neotropical species diversity is more ancient. This question is addressed using evolutionary rate analysis of sequence data of nuclear ribosomal internal transcribed spacers in diverse taxa occupying neotropical seasonally dry forests, includingRuprechtia(Polygonaceae), robinioid legumes (Fabaceae),ChaetocalyxandNissolia(Fabaceae), andLoxopterygium(Anacardiaceae). Species diversifications in these taxa occurred both during and before the Pleistocene in Central America, but were primarily pre–Pleistocene in South America. This indicates plausibility both for models that predict tropical species diversity to be recent and that invoke a role for Pleistocene climatic change, and those that consider it ancient and implicate geological factors such as the Andean orogeny and the closure of the Panama Isthmus. Cladistic vicariance analysis was attempted to identify common factors underlying evolution in these groups. In spite of the similar Mid–Miocene to Pliocene ages of the study taxa, and their high degree of endemism in the different fragments of South American dry forests, the analysis yielded equivocal, non–robust patterns of area relationships.
The impact of Quaternary Ice Ages on mammalian evolution
Authors: Lister Adrian M.
Published: April 2004

The Quaternary was a time of extensive evolution among mammals. Most living species arose at this time, and many of them show adaptations to peculiarly Quaternary environments. The latter include continental northern steppe and tundra, and the formation of lakes and offshore islands. Although some species evolved fixed adaptations to specialist habitats, others developed flexible adaptations enabling them to inhabit broad niches and to survive major environmental changes. Adaptation to short–term (migratory and seasonal) habitat change probably played a part in pre–adapting mammal species to the longer–term cyclical changes of the Quaternary. Fossil evidence indicates that environmental changes of the order of thousands of years have been sufficient to produce subspeciation, but speciation has typically required one hundred thousand to a few hundred thousand years, although there are both shorter and longer exceptions. The persistence of taxa in environments imposing strong selective regimes may have been important in forcing major adaptive change. Individual Milankovitch cycles are not necessarily implicated in this process, but nor did they generally inhibit evolutionary change among mammals: many evolutionary divergences built over multiple climatic cycles. Deduction of speciation timing requires input from fossils and modern phenotypic and breeding data, to complement and constrain mitochondrial DNA coalescence dates which appear commonly to overestimate taxic divergence dates and durations of speciation. Migrational and evolutionary responses to climate change are not mutually exclusive but, on the contrary, may be synergistic. Finally, preliminary analysis suggests that faunal turnover, including an important element of speciation, was elevated in the Quaternary compared with the Neogene, at least in some biomes. Macroevolutionary species selection or sorting has apparently resulted in a modern mammalian fauna enriched with fast–reproducing and/or adaptively generalist species.
Biodiversity informatics: managing and applying primary biodiversity data
Authors: Soberón Jorge , Peterson Townsend
Published: April 2004

Recently, advances in information technology and an increased willingness to share primary biodiversity data are enabling unprecedented access to it. By combining presences of species data with electronic cartography via a number of algorithms, estimating niches of species and their areas of distribution becomes feasible at resolutions one to three orders of magnitude higher than it was possible a few years ago. Some examples of the power of that technique are presented. For the method to work, limitations such as lack of high-quality taxonomic determination, precise georeferencing of the data and availability of high-quality and updated taxonomic treatments of the groups must be overcome. These are discussed, together with comments on the potential of these biodiversity informatics techniques not only for fundamental studies but also as a way for developing countries to apply state of the art bioinformatic methods and large quantities of data, in practical ways, to tackle issues of biodiversity management.
A taxonomic wish–list for community ecology
Authors: Gotelli Nicholas J.
Published: April 2004

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet–based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists.
Now is the time
Authors: Janzen Daniel H.
Published: April 2004

This is a commentary on the major challenges facing taxonomy in the twenty–first century, based on the author's experiences lobbying for the field over the years.
Towards a working list of all known plant species
Authors: Lughadha Eimear Nic
Published: April 2004

A complete listing of the world's known plant species has long been considered desirable but has remained an elusive target for generations of botanists. The adoption of the Global Strategy for Plant Conservation has reinforced the urgent need for a global plant checklist to support, facilitate and monitor the conservation and sustainable use of plant diversity worldwide. The increasing availability of large databases of biological information over the Internet has demonstrated that many of the obstacles to the collation and dissemination of vast, shared datasets can be overcome. We examine the challenges that still remain to be addressed if the botanical community is to achieve its ambitious objective of delivering a working list of all known plant species by 2010.
Introduction
Authors: Malhi Yadvinder , Phillips Oliver L.
Published: April 2004

This issue is based on the proceedings of a symposium on
‘Tropical Forests and Global Atmospheric Change’ that
was held at the Association for Tropical Biology annual
meeting in Panama City, Panama, in July 2002. Our overall
goal was to explore how the world's most biodiverse
ecosystems might fare in an era of rapid atmospheric
change. To achieve this we needed to ask original thinkers
from a wide range of disciplines to focus on this common
concern, often using new field data or new syntheses of
existing data. Several researchers who could not attend the
meeting were also invited to contribute to this Theme
Issue which builds on advances in several distinct scientific
disciplines.