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PubMed1997

Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence.

The extent of terrestrial vertebrate extinctions at the end of the Cretaceous is poorly understood, and estimates have ranged from a mass extinction to limited extinctions of specific groups. Molecular and paleontological data demonstrate that modern bird orders started diverging in the Early Cretaceous; at least 22 avian lineages of modern birds cross the Cretaceous-Tertiary boundary. Data for several other terrestrial vertebrate groups indicate a similar pattern of survival and, taken together, favor incremental changes during a Cretaceous diversification of birds and mammals rather than an explosive radiation in the Early Tertiary.

Animals↗

PubMed2005

Damage and repair of ancient DNA.

Under certain conditions small amounts of DNA can survive for long periods of time and can be used as polymerase chain reaction (PCR) substrates for the study of phylogenetic relationships and population genetics of extinct plants and animals, including hominids. Because of extensive DNA degradation, these studies are limited to species that lived within the past 10(4)-10(5) years (Late Pleistocene), although DNA sequences from 10(6) years have been reported. Ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes such as extinct horses, cave bears, the marsupial wolf, the moa, and Neanderthal. In the past few years, this technology has been extended to the study of infectious disease in ancient Egyptian and South American mummies, the dietary habits of ancient animals, and agricultural practices and population dynamics of early native Americans. Hence, ancient DNA contains information pertinent to numerous fields of study including evolution, population genetics, ecology, climatology, medicine, archeology, and behavior. The major obstacles to the study of aDNA are its extremely low yield, contamination with modern DNA, and extensive degradation. In the course of this review, we will discuss the current aDNA literature describing the importance of aDNA studies as they relate to important biological questions and the difficulties associated with extracting useful information from highly degraded and damaged substrates derived from limited sources. In addition, we will present some of our own preliminary and published data on mechanisms of DNA degradation and some speculative thoughts on strategies for repair and restoration of aDNA.

DNA↗

PubMed2006

Scale-free extinction dynamics in spatially structured host-parasitoid systems.

Much of the work on extinction events has focused on external perturbations of ecosystems, such as climatic change, or anthropogenic factors. Extinction, however, can also be driven by endogenous factors, such as the ecological interactions between species in an ecosystem. Here we show that endogenously driven extinction events can have a scale-free distribution in simple spatially structured host-parasitoid systems. Due to the properties of this distribution there may be many such simple ecosystems that, although not strictly permanent, persist for arbitrarily long periods of time. We identify a critical phase transition in the parameter space of the host-parasitoid systems, and explain how this is related to the scale-free nature of the extinction process. Based on these results, we conjecture that scale-free extinction processes and critical phase transitions of the type we have found may be a characteristic feature of many spatially structured, multi-species ecosystems in nature. The necessary ingredient appears to be competition between species where the locally inferior type disperses faster in space. If this condition is satisfied then the eventual outcome depends subtly on the strength of local superiority of one species versus the dispersal rate of the other.

Animals↗

PubMed2000

Nestedness, anti-nestedness, and the relationship between prevalence and intensity in ectoparasite assemblages of marine fish: a spatial model of species coexistence.

Nested species subset patterns consist in a hierarchical structure of species composition in related assemblages, with the species found in depauperate assemblages representing non-random subsets of progressively richer ones. This pattern has been found at the infracommunity level in about a third of the fish ectoparasite assemblages studied to date. Here we present evidence for another non-random structural pattern in assemblages of fish ectoparasites, anti-nestedness, which corresponds to situations in which parasite species are always absent from infracommunities richer than the most depauperate one in which they occur. We show that this pattern is exactly as common as nestedness, and that anti-nested assemblages are characterised by significantly lower prevalence and mean intensities of parasites than nested assemblages. In addition, we found a positive relationship between the prevalence and the mean intensity of parasites across the different assemblages. We propose a link between the nestedness/anti-nestedness continuum and the prevalence-intensity relationship that may involve colonisation-extinction processes. The results presented here suggest that, although nestedness may not be common in parasite communities, other departures from random species assembly are possible, and that some form of structure may be present in many communities. The continuum between nestedness and anti-nestedness also has implications for recent models of species coexistence in communities.

Animals↗

PubMed2001

Dynamic colloid--water partitioning of pyrene through a coastal Baltic spring bloom.

Colloidal organic particles constitute the dominant portion of particulate organic matter in surface seawater, but their influence on the phase speciation and bioavailability of hydrophobic organic compounds (HOCs) is sparsely evaluated. Studies on colloid-water partitioning have been focused on other regimes and have largely been performed on chemically defined subportions of total colloids such as the humic fraction. Available estimates of colloid-water partition coefficients (Kcoc) are highly variable and not easily explained by regularly applied Kow-Koc relationships. Here, pyrene was partitioned to bulk natural colloids isolated using cross-flow ultrafiltration techniques from the surface water of a coastal bay. A key objective was to elucidate biogeochemical controls on the changing colloid-sorbent qualities over the course of the dynamic allochtonous-autochtonous transition of a well-constrained boreal coastal spring bloom. The pyrene Kcoc was found to decrease from 12.9+/-0.9 x 10(3) Lw/kg(oc) in the terrestrial runoff dominated regime to values around 2.9+/-0.7 x 10(3) Lw/kg(oc), once phytoplankton production became the governing source of organic matter to the surface waters. The changing Kcoc was well correlated with the molar extinction coefficient at 280 nm of the colloidal organic carbon. This study supports other reports of an improved prediction of HOC phase speciation through this simple molecular proxy of the "quality" of organic sorbents. While being poor sorbents on a carbon atom basis, relative to soils and sediments, coastal marine colloids, by their shear abundance, may significantly attenuate the truly dissolved exposures of HOCs with log Kow above 5.

Absorption↗

PubMed2001

Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls.

Modern members of the mammalian order Cetacea (whales, dolphins and porpoises) are obligate aquatic swimmers that are highly distinctive in morphology, lacking hair and hind limbs, and having flippers, flukes, and a streamlined body. Eocene fossils document much of cetaceans' land-to-water transition, but, until now, the most primitive representative for which a skeleton was known was clearly amphibious and lived in coastal environments. Here we report on the skeletons of two early Eocene pakicetid cetaceans, the fox-sized Ichthyolestes pinfoldi, and the wolf-sized Pakicetus attocki. Their skeletons also elucidate the relationships of cetaceans to other mammals. Morphological cladistic analyses have shown cetaceans to be most closely related to one or more mesonychians, a group of extinct, archaic ungulates, but molecular analyses have indicated that they are the sister group to hippopotamids. Our cladistic analysis indicates that cetaceans are more closely related to artiodactyls than to any mesonychian. Cetaceans are not the sister group to (any) mesonychians, nor to hippopotamids. Our analysis stops short of identifying any particular artiodactyl family as the cetacean sister group and supports monophyly of artiodactyls.

Animals↗

PubMed1972

Competition, competitive repulsion, and coexistence.

This manuscript is concerned with concepts rather than abstruse details or mathematics. Discussed are: competition; extended competition, proposed for competition in the strict sense, extended and modified by all related interactions including predation, parasitism, disease, and even cooperation, all of which can be "weapons of competition"; competitive repulsion, proposed for the sum of forces that determine spacings, including ecologic spacings, of individuals and populations; Darwin (biotic) equilibriums; competitive extinction, Gause's principle, limited and limiting resources, and single-resource competition; de facto coexistence of competing species, exemplified by green plants competing for sunlight; niche competition; the two concepts of competitive exclusion; devision of resources and of their utilizers; cause and effect in real situations; and niches, niche overlap, and coexistence. Stressed is the complexity of the real world, and the confusion that can and does arise from modeling it too simply.

Biological Evolution↗

PubMed2002

On the evolution of cytoplasmic incompatibility in haplodiploid species.

The most enigmatic sexual manipulation by Wolbachia endosymbionts is cytoplasmic incompatibility (CI): infected males are reproductively incompatible with uninfected females. In this paper, we extend the theory on population dynamics and evolution of CI, with emphasis on haplodiploid species. First, we focus on the problem of the threshold to invasion of the Wolbachia infection in a population. Simulations of the dynamics of infection in small populations show that it does not suffice to assume invasion by drift alone (or demographic "accident"). We propose several promising alternatives that may facilitate invasion of Wolbachia in uninfected populations: sex-ratio effects, meta population structure, and other fitness-compensating effects. Including sex-ratio effects of Wolbachia allows invasion whenever infected females produce more infected daughters than uninfected females produce uninfected daughters. Several studies on haplodiploid species suggest the presence of such sex-ratio effects. The simple metapopulation model we analyzed predicts that, given that infecteds are better "invaders," uninfecteds must be better "colonizers" to maintain coexistence of infected and uninfected patches. This condition seems more feasible for species that suffer local extinction due to predation (or parasitization) than for species that suffer local extinction due to overexploiting their resource(s). Finally, we analyze the evolution of CI in haplodiploids once a population has been infected. Evolution does not depend on the type of CI (female mortality or male production), but hinges solely on decreasing the fitness cost and/or increasing the transmission efficiency. Our models offer new perspectives for increasing our understanding of the population and evolutionary dynamics of CI.

Bacterial Infections↗

PubMed1985

Purification, amino-acid sequence and some properties of the ferredoxin isolated from Bacillus acidocaldarius.

Ferredoxin was isolated from the aerobic, thermophilic and acidophilic bacterium Bacillus acidocaldarius and its sequence of 78 amino acids completely determined by automated Edman degradation of the protein and of peptides derived from chemical cleavage between aspartic acid and proline and from enzymatic digestions. The optical spectrum of the oxidized protein has a broad maximum around 400 nm. The ferredoxin is thermostable: its absorbance begins to decrease only at incubation over 71 degrees C. The number of iron and inorganic sulphur atoms per molecule was determined to be 5.3 and 5.0, respectively. The calculated molar extinction coefficient was 23 000 M-1 X cm-1, the molecular mass of the apoferredoxin 8 872 Da. Contrary to all expectations, the sequence of B. acidocaldarius ferredoxin shows very little homology to that of B. stearothermophilus but closely resembles that of Thermus thermophilus.

Amino Acid Sequence↗

PubMed1978

Cellular and molecular studies on globin gene expression.

Globin gene expression has been studied with the use of a combination of cell and molecular biology techniques. With a somatic cell hybrid between mouse erythroleukemia (MEL) and human erythroid cells, human and mouse globin genes can be coexpressed in the same hybrid cell. Somatic cell hybridization between MEL cells and nonerythroid cells (e.g., human fibroblasts) results in hybrid cells that cannot be induced to produce hemoglobin of any type. Molecular hybridization of cellular DNA and RNA with globin cDNA indicates that the globin genes are present but that no globin mRNA is in the nonexpressing hybrid cell. This finding demonstrates that the loss of globin gene expression in the hybrid cell occurs at the level of transcription or mRNA processing. The nucleus of the nonerythroid cell is not necessary for the extinction of globin gene expression, since cybrids formed from MEL cells with enucleated nonerythroid cells also result in cells which cannot be induced to synthesize hemoglobin even after 40 or more generations. These data suggest that the cytoplasm of cells contains diffusible regulatory molecules which influence globin gene expression. In our attempt to develop an intracellular assay to test for regulatory molecules, we studied the procedure microinjection with red blood cell (RBC) ghosts. Rabbit globin mRNA (with hemin) was loaded into RBC's and then, by Sendai virus-mediated fusion, into Chinese hamster ovary (CHO) cells growing in culture; these microinjected CHO cells synthesized hemoglobin. Since this microinjection procedure appears to be effective in inserting both proteins and nucleic acids into intact cells, it should be possible to develop modifications for inserting aliquots of fractionated cytoplasm into growing cells. The procedure might then be useful as an assay for putative genetic regulatory molecules.

Animals↗

PubMed2005

Assessment of urine and fecal testosterone metabolite excretion in Chinchilla lanigera males.

Endemic chinchilla (Chinchilla spp.) populations are nearly extinct in the wild (South America). In captive animals (Chinchilla lanigera and C. brevicaudata), reproduction is characterized by poor fertility and limited by seasonal breeding patterns. Techniques applied for studying male reproductive physiology in these species are often invasive and stressful (i.e. repeated blood sampling for sexual steroids analysis). To evaluate endocrine testicular function, the present experiments were designed to (a) determine the main route of testosterone excretion (14C-testosterone infusion in four males); (b) validate urine and fecal testosterone metabolite measurements (HPLC was used to separate metabolites and immunoreactivity was assessed in all metabolites using a commercial testosterone radioimmunoassay, and parallelism, accuracy and precision tests were conducted to validate the immunoassay); and (c) investigate the biological relevance of the techniques applied (quantification of testosterone metabolite excretion into urine and feces from five males injected with hCG and comparison between 10 males and 10 females). Radiolabelled metabolites of 14C-testosterone were excreted, 84.7+/-4.2 % in urine and 15.2+/-3.9 % in feces. A total of 82.7+/-4.2% of urinary and 45.7+/-13.6% of fecal radioactivity was excreted over the first 24 h period post-infusion (metabolite concentration peaked at 8.2+/-2.5 h and 22.0+/-7.0 h, respectively). Several urinary and fecal androgen metabolites were separated by HPLC but only fecal metabolites were associated with native testosterone; however, there was immunoreactivity in more than one metabolite derived from 14C-testosterone. After hCG administration, an increase in androgen metabolite excretion was observed (p<0.05). Males excreted greater amounts daily of urinary androgen metabolites as compared with females (p<0.05); this difference was not evident in feces. Results of the present study indicate that the procedure used is a reliable and non-invasive method to repeatedly monitor variations in testicular endocrine activity in this species. It can be a useful tool that would help ensure the survival of the wild populations as well as to provide the basis for a more efficient use by the fur industry.

Androgens↗

PubMed2000

Introduction, persistence and fade-out of porcine reproductive and respiratory syndrome virus in a Dutch breeding herd: a mathematical analysis.

The objective of this study was to investigate the dynamics of PRRSV infection and to quantify transmission within a breeding herd, and its impact on herd performance. For this purpose a longitudinal study was performed in a closed breeding herd of 115 sows. Statistical methods and Monte Carlo simulations based on stochastic SIR models were used to analyse the observational data. Moreover, a case-control study was performed to determine whether seroconversion of sows during gestation was associated with aberrant litters. The transmission parameter R was estimated to be 3.0 (95% confidence interval 1.5-6.0) for the model version based on the most plausible assumptions that the infectious period lasts 56 days and no lifelong immunity exists after infection. Based on simulations using a breeding herd of equal size the average time-to-extinction was estimated to be 6 years; using a herd of twice the size, it was 80 years. Furthermore, in contrast to the epidemic phase of the disease, the endemic phase was not detrimental to herd performance.

Animals↗

PubMed2001

Late Cretaceous relatives of rabbits, rodents, and other extant eutherian mammals.

Extant eutherian mammals and their most recent common ancestor constitute the crown group Placentalia. This taxon, plus all extinct taxa that share a more recent common ancestor with placentals than they do with Metatheria (including marsupials), constitute Eutheria. The oldest well documented eutherian-dominated fauna in the world is Dzharakuduk, Uzbekistan. Among eutherians that it yields is Kulbeckia, an 85-90-Myr-old member of Zalambdalestidae (a family of Late Cretaceous Asian eutherians). This extends Zalambdalestidae back by some 10 million years from sites in the Gobi Desert, Mongolia. A phylogenetic analysis of well described Late Cretaceous eutherians strongly supports Zalambdalestidae, less strongly supports 'Zhelestidae' (a Late Cretaceous clade related to Tertiary ungulates), but does not support Asioryctitheria (a group of Late Cretaceous Asian eutherians). A second analysis incorporating placentals from clades that include rodents (Tribosphenomys), lagomorphs (Mimotona) and archaic ungulates (Protungulatum and Oxyprimus) strongly supports Zalambdalestidae in a clade with Glires (rabbits, rodents and extinct relatives) and less strongly 'Zhelestidae' within a clade that includes archaic ungulates ('condylarths'). This argues that some Late Cretaceous eutherians belong within the crown group Placentalia. The ages of these taxa are in line with molecularly based estimates of 64-104 Myr ago (median 84 Myr ago) for the superordinal diversification of some placentals, but provide no support for a Late Cretaceous diversification of extant placental orders.

Animals↗

PubMed2005

Bite club: comparative bite force in big biting mammals and the prediction of predatory behaviour in fossil taxa.

We provide the first predictions of bite force (BS) in a wide sample of living and fossil mammalian predators. To compare between taxa, we calculated an estimated bite force quotient (BFQ) as the residual of BS regressed on body mass. Estimated BS adjusted for body mass was higher for marsupials than placentals and the Tasmanian devil (Sarcophilus harrisii) had the highest relative BS among extant taxa. The highest overall BS was in two extinct marsupial lions. BFQ in hyaenas were similar to those of related, non-osteophagous taxa challenging the common assumption that osteophagy necessitates extreme jaw muscle forces. High BFQ in living carnivores was associated with greater maximal prey size and hypercarnivory. For fossil taxa anatomically similar to living relatives, BFQ can be directly compared, and high values in the dire wolf (Canis dirus) and thylacine (Thylacinus cynocephalus) suggest that they took relatively large prey. Direct inference may not be appropriate where morphologies depart widely from biomechanical models evident in living predators and must be considered together with evidence from other morphological indicators. Relatively low BFQ values in two extinct carnivores with morphologies not represented among extant species, the sabrecat, Smilodon fatalis, and marsupial sabretooth, Thylacosmilus atrox, support arguments that their killing techniques also differed from extant species and are consistent with 'canine-shear bite' and 'stabbing' models, respectively. Extremely high BFQ in the marsupial lion, Thylacoleo carnifex, indicates that it filled a large-prey hunting niche.

Animals↗

PubMed2000

The evolution of filial cannibalism and female mate choice strategies as resolutions to sexual conflict in fishes.

Filial cannibalism (the consumption of one's own viable offspring) is common among fish with paternal care. In this study, I use a computer simulation to study simultaneous evolution of male filial cannibalism and female mate choice. Under certain conditions, selection on parental males favors filial cannibalism. When filial cannibalism increases a male's probability to raise the current brood successfully, filial cannibalism also benefits the female. However, when egg eating is a male investment into future reproduction, a conflict between female and male interests emerges. Here I investigate how female discrimination against filial cannibals affects evolution of filial cannibalism and how different female choice criteria perform against filial cannibalism. The introduction of discriminating females makes the fixation of filial cannibalism less likely. I introduced three different female choice criteria: (1) females who could discern a male's genotype, that is, whether the male was going to eat eggs as an investment in future reproductive events; (2) energy-choosing females that preferred to mate with males who had enough energy reserves to live through the current brood cycle without consuming eggs; and (3) females that preferred to mate with already mated males, that is, males with eggs in their nest. Genotype choice never coexisted with filial cannibals at fixation and filial cannibals were unable to invade a population with genotype-choosing females. Energy choice was successful only when males had high energy reserves and were less dependent on filial cannibalism as an alternative energy source. The egg choosers frequently coexisted with the cannibals at fixation. When the female strategies were entered simultaneously, the most frequent outcome for low mate sampling costs was that both the cannibals and the egg choice was fixed and all other strategies went extinct. These results suggest that sexual conflicts may not always evolve toward a resolution of the conflict, but sometimes the stable state retains the conflict. In the present case, this was because the egg-preference strategy had a higher fitness than the other female strategies. The outcome of this simulation is similar to empirical findings. In fish with paternal care, male filial cannibalism and female preference for mates with eggs commonly co-occur.

Animals↗

PubMed2004

Exclusive consolidated memory phases in Drosophila.

Two types of consolidated memory have been described in Drosophila, anesthesia-resistant memory (ARM), a shorter-lived form, and stabilized long-term memory (LTM). Until now, it has been thought that ARM and LTM coexist. On the contrary, we show that LTM formation leads to the extinction of ARM. Flies devoid of mushroom body vertical lobes cannot form LTM, but spaced conditioning can still erase their ARM, resulting in a remarkable situation: The more these flies are trained, the less they remember. We propose that ARM acts as a gating mechanism that ensures that LTM is formed only after repetitive and spaced training.

Adenylyl Cyclases↗

PubMed1978

The epidemic in a closed population with all susceptibles equally vulnerable; some results for large susceptible populations and small initial infections.

Kendall's (1956) approach to the 'general' epidemic is generalized by dropping the assumptions of constant infectivity and random recovery or death of ill individuals. A great deal of attention is paid to the biological background and the heuristics of the model formulation. Some new results are: (1) the derivation of Kermack's and McKendrick's integral equation from what seems to be the most general set of assumptions in section 2.2, (2) the use of Kermack's and McKendrick's final value equation to arrive at a finite time version of the threshold theorem for the general case, comparable to the for the case of only one Markovian state of illness in section 2.5, (3) the analysis of the behaviour of the solutions of the integral equation when the starting infection approaches zero in section 2.7, (4) the derivation of the probability structure of a general branching process, after conditioning on extinction in section 3.6, (5) the statement of the generalized versions of Kendall's ideas in the form of precise limit conjectures in section 4, (6) the derivation of a closed expression for the limit epidemic resulting from (3) in appendix 4.

Disease Outbreaks↗

PubMed2003

Establishment success and extinction risk in autocorrelated environments.

We consider establishment success (and extinction risk of small populations) in fluctuating environments, by means of an inhomogeneous branching process model. In this model it is assumed that individuals reproduce asexually during discrete reproduction periods. Within each period individuals reproduce independently and have random numbers of offspring. Expected numbers of offspring vary over reproduction periods due to random environmental changes. Previous simulation results indicated that there is a positive autocorrelation between the establishment probabilities of invaders in successive reproduction periods when environmental states are independently distributed. This result was never formally proved. In this paper we prove that this is indeed true, regardless of the form of the distribution of environmental states or the offspring distribution (under a monotonicity condition, which holds for biologically realistic models). Furthermore, we prove that it is also true for positively autocorrelated environmental states. We show by a counterexample that in environments with a strong negative autocorrelation establishment probabilities can be negatively autocorrelated. This was further examined through simulations. Our results imply that in independent, positively autocorrelated and weakly negatively autocorrelated environments the probability of success of invasion in different independently varying sites is the highest, followed by sequential invasion. For environments with a strong negative autocorrelation, sequential invasion has the highest probability of success. Effects of autocorrelation were further examined with simulations. From the results it appears that the expected length of 'runs of bad luck' is the most crucial factor for establishment success.

Algorithms↗