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PubMed2006

Physiological constraints on organismal response to global warming: Mechanistic insights from clinally varying populations and implications for assessing endangerment.

Recent syntheses indicate that global warming affects diverse biological processes, but also highlight the potential for some species to adapt behaviourally or evolutionarily to rapid climate change. Far less attention has addressed the alternative, that organisms lacking this ability may face extinction, a fate projected to befall one-quarter of global biodiversity. This conclusion is controversial, in part because there exist few mechanistic studies that show how climate change could precipitate extinction. We provide a concrete, mechanistic example of warming as a stressor of organisms that are closely adapted to cool climates from a comparative analysis of organismal tolerance among clinally varying populations along a natural thermal gradient. We found that two montane salamanders exhibit significant metabolic depression at temperatures within the natural thermal range experienced by low and middle elevation populations. Moreover, the magnitude of depression was inversely related to native elevation, suggesting that low elevation populations are already living near the limit of their physiological tolerances. If this finding generally applies to other montane specialists, the prognosis for biodiversity loss in typically diverse montane systems is sobering. We propose that indices of warming-induced stress tolerance may provide a critical new tool for quantitative assessments of endangerment due to anthropogenic climate change across diverse species.

Animals↗
PubMed1996

Multiple factors in the origin of the Cretaceous/Tertiary boundary: the role of environmental stress and Deccan Trap volcanism.

A review of the scenarios for the Cretaceous/ Tertiary (K/T) boundary event is presented and a coherent hypothesis for the origin of the event is formulated. Many scientists now accept that the event was caused by a meteorite impact at Chicxulub in the Yucatan Peninsula, Mexico. Our investigations show that the oceans were already stressed by the end of the Late Cretaceous as a result of the long-term drop in atmospheric CO2, the long-term drop in sea level and the frequent development of oceanic anoxia. Extinction of some marine species was already occurring several million years prior to the K/T boundary. The biota were therefore susceptible to change. The eruption of the Deccan Traps, which began at 66.2 Ma, coincides with the K/T boundary events. It erupted huge quantities of H2SO4, HCl, CO2, dust and soot into the atmosphere and led to a significant drop in sea level and marked changes in ocean temperature. The result was a major reduction in oceanic productivity and the creation of an almost dead ocean. The volcanism lasted almost 0.7 m.y. Extinction of biological species was graded and appeared to correlate with the main eruptive events. Elements such as Ir were incorporated into the volcanic ash, possibly on soot particles. This horizon accumulated under anoxic conditions in local depressions and became the marker horizon for the K/T boundary. An oxidation front penetrated this horizon leading to the redistribution of elements. The eruption of the Deccan Traps is the largest volcanic event since the Permian-Triassic event at 245 Ma. It followed a period of 36 m.y. in which the earth's magnetic field failed to reverse. Instabilities in the mantle are thought to be responsible for this eruption and therefore for the K/T event. We therefore believe that the K/T event can be explained in terms of the effects of the Deccan volcanism on an already stressed biosphere. The meteorite impact at Chicxulub took place after the onset of Deccan volcanism. It probably played a regional, rather than global, role in the K/T extinction.

Atmosphere↗
PubMed2003

The relationships between taxonomy and conservation biology in the century of extinctions.

The 21st century will be that of the crisis of biodiversity and of extinctions: a majority of the planet's species might disappear before having even been studied by man. The discipline in charge of this study, taxonomy, is currently facing severe problems, concerning its status inside biology and its relationships with conservation biology. Yet taxonomy and conservation biology would have much to gain to becoming allies rather than largely foreign disciplines. This would require some important changes in mentality and behaviour.

Biodiversity↗
PubMed2025

Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.

Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.

Animals↗
PubMed2026

Genomic erosion in the assessment of species' extinction risk and recovery potential.

Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the International Union for Conservation of Nature Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the International Union for Conservation of Nature Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.

Extinction, Biological↗
PubMed2005

A cryptic taxon of Galápagos tortoise in conservation peril.

As once boldly stated, 'bad taxonomy can kill', highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention.

Animals↗
PubMed2006

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Animals↗
PubMed2006

Invasion of an asexual American water flea clone throughout Africa and rapid displacement of a native sibling species.

The huge ecological and economic impact of biological invasions creates an urgent need for knowledge of traits that make invading species successful and factors helping indigenous populations to resist displacement by invading species or genotypes. High genetic diversity is generally considered to be advantageous in both processes. Combined with sex, it allows rapid evolution and adaptation to changing environments. We combined paleogenetic analysis with continent-wide survey of genetic diversity at nuclear and mitochondrial loci to reconstruct the invasion history of a single asexual American water flea clone (hybrid Daphnia pulexxDaphnia pulicaria) in Africa. Within 60 years of the original introduction of this invader, it displaced the genetically diverse, sexual population of native D. pulex in Lake Naivasha (Kenya), despite a formidable numerical advantage of the local population and continuous replenishment from a large dormant egg bank. Currently, the invading clone has spread throughout the range of native African D. pulex, where it appears to be the only occurring genotype. The absence of genetic variation did not hamper either the continent-wide establishment of this exotic lineage or the effective displacement of an indigenous and genetically diverse sibling species.

Africa↗
PubMed2004

Vanishing flora--lost chemistry: the scents of endangered plants around the world.

As part of our broad and ongoing evaluation of the olfactory components of fragrant plants and flowers during the past 25 years, we have encountered an astounding number of interestingly scented, but endangered plant species. In appreciation of nature's marvels in these species, we are compiling a report on their scent compositions and complementary information in an upcoming book 'Vanishing Flora--Lost Chemistry'. In this paper, a few examples of endangered plant species and their scent components are presented as a brief introduction to the concept of the book project.

Animals↗
PubMed2006

[An introduction into bioethics and parasitology].

Bioethical considerations increasingly affect the process of integrating scientific and medical findings into the moral conceivabilities of a society and, consequentially, into the stock of laws. In a natural science like parasitology a social consensus must be reached in the areas of species protection, of the red biotechnology, of human prenatal diagnosis, and of animal experiments. The crucial problem is the social value of an individual's dignity and the conjoined question of the admissibility of an exploitation of a creature. The responsibility of man for other organisms, in that particular case parasites and their hosts, is brought up for discussion in a bioethic debate.

Animal Experimentation↗
PubMed2006

Major histocompatibility complex variation in the endangered crested ibis Nipponia nippon and implications for reintroduction.

The major histocompatibility complex (MHC), with its extraordinary levels of genetic variation, is thought to be an essential aspect of the ability of an organism to recognize different parasites and pathogens. It has also been proposed to regulate reproductive processes in many aspects. Here we examine the genetic variation of the second exon of the MHC class II B genes of the crested ibis, an endangered species known to descend from just two breeding pairs rediscovered in 1981. Only five alleles are identified by single-strand conformation polymorphism (SSCP) analysis of 36 samples taken from both wild and captive populations, and a comparatively low level of divergence between MHC alleles is observed. We suggest that representative sampling of individuals with most of the different MHC allele genotypes to constitute a founder population, together with the monitoring of the pathogen status of candidate sites before release, is of great importance for raising the success rate of reintroduction for the crested ibis.

Amino Acid Sequence↗
PubMed2006

Monitoring of the endangered Pinna nobilis Linné, 1758 in the Mar Grande of Taranto (Ionian Sea, Italy).

The present study aimed to improve the knowledge of the bivalve Pinna nobilis L. population distribution in Mar Grande of Taranto (Ionian Sea). Although historical references report the local abundant presence of this endangered species, there is a lack of updated information about its exact distribution. For this purpose, a visual census of P. nobilis was performed by SCUBA diving in the Mar Grande basin from September 2004 to March 2005. Pinnids were found at depths from 3 to 16 m, with a density ranging from 0.1 to 0.7 ind ha(-1). The survey method employed in this study was non-destructive, relatively simple to perform and easily applicable for monitoring studies. Field data were stored in a database and linked with the study area by means of the GIS technology. The results of the present study indicate a tentative of recovery of P. nobilis population in Mar Grande in spite of all the difficulties of a degraded and heavily polluted environment and the damages of illegal fishing methods.

Animals↗
PubMed2006

A preliminary risk assessment of organochlorines accumulated in fish to the Indo-Pacific humpback dolphin (Sousa chinensis) in the Northwestern waters of Hong Kong.

The Indo-Pacific humpback dolphin is considered threatened due to several factors including pollution in Hong Kong and the risks due to consumption of fish tainted with polychlorinated biphenyls (PCBs) and organochlorine pesticides were assessed. Six species of fish Collichthys lucida, Pseudosciaena crocea, Johnius sp., Thryssa sp., Mugil sp. and Trichiurus sp., which comprise the main prey species of humpback dolphins were collected for analyses. Risks due to total PCBs, total TEQs, PCB 118 and the pesticides were assessed with the use of toxicity reference values as the threshold reference benchmarks. The calculated risk quotients (RQs) showed that the risks associated with organochlorines were generally low. The highest RQ was associated with total TEQs suggesting that dioxin-like PCBs may pose the highest risk to the dolphins. The HCHs, total PCBs and heptachlor had comparatively high RQs and thus they should also be the priority organochlorines that would require further investigation.

Animals↗
PubMed2006

Mitochondrial DNA identification of game and harvested freshwater fish species.

The use of DNA in forensics has grown rapidly for human applications along with the concomitant development of bioinformatics and demographic databases to help fully realize the potential of this molecular information. Similar techniques are also used routinely in many wildlife cases, such as species identification in food products, poaching and the illegal trade of endangered species. The use of molecular techniques in forensic cases related to wildlife and the development of associated databases has, however, mainly focused on large mammals with the exception of a few high-profile species. There is a need to develop similar databases for aquatic species for fisheries enforcement, given the large number of exploited and endangered fish species, the intensity of exploitation, and challenges in identifying species and their derived products. We sequenced a 500bp fragment of the mitochondrial cytochrome b gene from representative individuals from 26 harvested fish taxa from Ontario, Canada, focusing on species that support major commercial and recreational fisheries. Ontario provides a unique model system for the development of a fish species database, as the province contains an evolutionarily diverse array of freshwater fish families representing more than one third of all freshwater fish in Canada. Inter- and intraspecific sequence comparisons using phylogenetic analysis and a BLAST search algorithm provided rigorous statistical metrics for species identification. This methodology and these data will aid in fisheries enforcement, providing a tool to easily and accurately identify fish species in enforcement investigations that would have otherwise been difficult or impossible to pursue.

Animals↗
PubMed2006

Sustainable ecosystem management using optimal control theory: part 2 (stochastic systems).

Sustainable development of ecosystems through external ecosystem management is assuming importance for the environmentalists. To that effect, previous work by the authors looked at the option of manipulating population dynamics of the species in an ecosystem to achieve sustainability. Fisher information is used as the quantifying measure of sustainability and optimal control theory is used to derive the control profiles. However, that work considered only deterministic systems. Uncertainty being prevalent in all systems, particularly in natural systems, this paper extends that work to analyse uncertain systems. Predator-prey models are used to model the species populations and different control philosophies are compared. Ito mean reverting process is used to model the stochastic process, and stochastic maximum principle is used to derive the control profiles. The results for the objective of FI variance minimization qualitatively agree with those for the deterministic system, while the results for the FI maximization objective differ. It is observed that the instability associated with the FI maximization objective for deterministic systems is absorbed by the noise introduced by the uncertainty. Quantitatively, it is observed that the degree of uncertainty, along with its presence, is also important to identify the most appropriate management strategy.

Animals↗
PubMed2006

Sustainable ecosystem management using optimal control theory: part 1 (deterministic systems).

The concept of sustainability, an abstract one by its nature, has been given a mathematical representation through the use of Fisher information as a measure. It is used to propose the sustainability hypotheses for dynamical systems, which has paved the way to achieve sustainable development through externally enforced control schemes. For natural systems, this refers to the task of ecosystem management, which is complicated due the lack of clear objectives. This work attempts to incorporate the idea of sustainability in ecosystem management. The natural regulation of ecosystems suggests two possible control options, top-down control and bottom-up control. A comparison of these two control philosophies is made on generic food chain models using the objectives derived from the sustainability hypotheses. Optimal control theory is used to derive the control profiles to handle the complex nature of the models and the objectives. The results indicate a strong relationship between the hypotheses and the dynamic behavior of the models, supporting the use of Fisher information as a measure. As regards to ecosystem management, it has been observed that top-down control is more aggressive but can result in instability, while bottom-up control is guaranteed to give a stable and improved dynamic response. The results also indicate that bottom-up control is a better option to affect shifts in the dynamic regimes of a system, which may be required to recover the system from a natural disaster like the hurricane Katrina.

Animals↗
PubMed2006

Persistence despite perturbations for interacting populations.

Two definitions of persistence despite perturbations in deterministic models are presented. The first definition, persistence despite frequent small perturbations, is shown to be equivalent to the existence of a positive attractor i.e. an attractor bounded away from extinction. The second definition, persistence despite rare large perturbations, is shown to be equivalent to permanence i.e. a positive attractor whose basin of attraction includes all positive states. Both definitions set up a natural dichotomy for classifying models of interacting populations. Namely, a model is either persistent despite perturbations or not. When it is not persistent, it follows that all initial conditions are prone to extinction due to perturbations of the appropriate type. For frequent small perturbations, this method of classification is shown to be generically robust: there is a dense set of models for which persistent (respectively, extinction prone) models lies within an open set of persistent (resp. extinction prone) models. For rare large perturbations, this method of classification is shown not to be generically robust. Namely, work of Josef Hofbauer and the author have shown there are open sets of ecological models containing a dense sets of permanent models and a dense set of extinction prone models. The merits and drawbacks of these different definitions are discussed.

Animals↗
PubMed2005

Itô versus Stratonovich calculus in random population growth.

The context is the general stochastic differential equation (SDE) model dN/dt=N(g(N)+sigmaepsilon(t)) for population growth in a randomly fluctuating environment. Here, N=N(t) is the population size at time t, g(N) is the 'average' per capita growth rate (we work with a general almost arbitrary function g), and sigmaepsilon(t) is the effect of environmental fluctuations (sigma>0, epsilon(t) standard white noise). There are two main stochastic calculus used to interpret the SDE, Itô calculus and Stratonovich calculus. They yield different solutions and even qualitatively different predictions (on extinction, for example). So, there is a controversy on which calculus one should use. We will resolve the controversy and show that the real issue is merely semantic. It is due to the informal interpretation of g(x) as being an (unspecified) 'average' per capita growth rate (when population size is x). The implicit assumption usually made in the literature is that the 'average' growth rate is the same for both calculi, when indeed this rate should be defined in terms of the observed process. We prove that, when using Itô calculus, g(N) is indeed the arithmetic average growth rate R(a)(x) and, when using Stratonovich calculus, g(N) is indeed the geometric average growth rate R(g)(x). Writing the solutions of the SDE in terms of a well-defined average, R(a)(x) or R(g)(x), instead of an undefined 'average' g(x), we prove that the two calculi yield exactly the same solution. The apparent difference was due to the semantic confusion of taking the informal term 'average growth rate' as meaning the same average.

Algorithms↗