Complementary predation on metamorphosing species promotes stability in predator–prey systems

Functionally redundant predation and functionally complementary predation are both widespread phenomena in nature. Functional complementary predation can be found, for example, when predators feed on different life stages of their prey, while functional redundant predation occurs when different predators feed on all life stages of a shared prey. Both phenomena are common in nature, and the extent of differential life-stage predation depends mostly on prey life history; complementary predation is expected to be more common on metamorphosing prey species, while redundant predation is thought to be higher on non-metamorphosing species. We used an ordinary differential equation model to explore the effect of varying degree of complementary and redundant predation on the dynamic properties of a system with two predators that feed on an age-structured prey. Our main finding was that predation on one stage (adult or juvenile) resulted in a more stable system (i.e., it is stable for a wider range of parameters) compared to when the two predators mix the two prey developmental stages in their diet. Our results demonstrate that predator–prey dynamics depends strongly on predators' functionality when predator species richness is fixed. Results also suggest that systems with metamorphosing prey are expected to be more diverse compared to systems with non-metamorphosing prey.     

Beyond “greening” and “browning”: Trends in grassland ground cover fractions across Eurasia that account for spatial and temporal autocorrelation

Grassland ecosystems cover up to 40% of the global land area and provide many ecosystem services directly supporting the livelihoods of over 1 billion people. Monitoring long-term changes in grasslands is crucial for food security, biodiversity conservation, achieving Land Degradation Neutrality goals, and modeling the global carbon budget. Although long-term grassland monitoring using remote sensing is extensive, it is typically based on a single vegetation index and does not account for temporal and spatial autocorrelation, which means that some trends are falsely identified while others are missed. Our goal was to analyze trends in grasslands in Eurasia, the largest continuous grassland ecosystems on Earth. To do so, we calculated Cumulative Endmember Fractions (annual sums of monthly ground cover fractions) derived from MODIS 2002–2020 time series, and applied a new statistical approach PARTS that explicitly accounts for temporal and spatial autocorrelation in trends. We examined trends in green vegetation, non-photosynthetic vegetation, and soil ground cover fractions considering their independent change trajectories and relations among fractions over time. We derived temporally uncorrelated pixel-based trend maps and statistically tested whether observed trends could be explained by elevation, land cover, SPEI3, climate, country, and their combinations, all while accounting for spatial autocorrelation. We found no statistical evidence for a decrease in vegetation cover in grasslands in Eurasia. Instead, there was a significant map-level increase in non-photosynthetic vegetation across the region and local increases in green vegetation with a concomitant decrease in soil fraction. Independent environmental variables affected trends significantly, but effects varied by region. Overall, our analyses show in a statistically robust manner that Eurasian grasslands have changed considerably over the past two decades. Our approach enhances remote sensing-based monitoring of trends in grasslands so that underlying processes can be discerned.     

Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens

New quantitative methods are applied to the 135 human mitochondrial sequences from the Vigilant et al. data set. General problems in analyzing large numbers of short sequences are discussed, and an improved strategy is suggested. A key feature is to focus not on individual trees but on the general "landscape" of trees. Over 1,000 searches were made from random starting trees with only one tree (a local optimum) being retained each time, thereby ensuring optima were found independently. A new tree comparison metric was developed that is unaffected by rearrangements of trees around many very short internal edges. Use of this metric showed that downweighting hypervariable sites revealed more evolutionary structure than studies that weighted all sites equally. Our results are consistent with convergence toward a global optimum. Crucial features are that the best optima show very strong regional differentiation, a common group of 49 African sequences is found in all the best optima, and the best optima contain the 16 !Kung sequences in a separate group of San people. The other 86 sequences form a heterogeneous mixture of Africans, Europeans, Australopapuans, and Asians. Thus all major human lineages occur in Africa, but only a subset occurs in the rest of the world. The existence of these African-only groups strongly contradicts multiregional theories for the origin of Homo sapiens that require widespread migration and interbreeding over the entire range of H. erectus. Only when the multiregional model is rejected is it appropriate to consider the root, based on a single locus, to be the center of origin of a population (otherwise different loci could give alternative geographic positions for the root). For this data, several methods locate the root within the group of 49 African sequences and are thus consistent with the recent African origin of H. sapiens. We demonstrate that the time of the last common ancestor cannot be the time of major expansion in human numbers, and our results are thus also consistent with recent models that differentiate between the last common ancestor, expansion out of Africa, and the major expansion in human populations. Such a two-phase model is consistent with a wide range of molecular and archeological evidence.      

A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.      

Bin classification of G-protein-coupled peptide receptors

Summary With the use of the binmap method, 154 G-protein-coupled peptide receptors are classified. The binmap coordinates are obtained by using the number of residues between the conserved N residue in TM1 and C in the TM4-TM5 loop, between this C and the conserved P in TM6, and between this P and the last residue of the sequence. The binmap suggests that the cloned fMLP receptor in rabbit belongs in fact to the IL8 receptor type.     

Increased incidence of micronuclei assessed with the micronucleus assay and the fluorescence in situ hybridization (FISH) technique in peripheral blood lymphocytes of nurses exposed to nitrous oxide

It has been postulated that exposure to nitrous oxide and halogenated anaesthetics is associated with various adverse health effects such as neurological and reproductive abnormalities or impairment of hepatic functions. In spite of the quite well known genotoxic effects of exposure to nitrous oxide in vivo, the mechanisms of these effects are still not clear. The aim of this study was to assess the frequency of micronuclei and to identify the type of chromosomal damage (clastogenic or aneugenic) in peripheral blood lymphocytes of operating-room nurses exposed to nitrous oxide. The study group comprised 46 women working at departments where the concentration of nitrous oxide ranged from 14 to 2308 mg/m3. The control population was composed of 28 women employed in the same hospitals but in non-surgical departments. The clastogenic/aneugenic effect of nitrous oxide was evaluated in lymphocytes using the standard micronucleus (MN) assay in combination with the fluorescence in situ hybridization (FISH) technique with pancentromeric probes. The results show a significant increase of the MN frequency in lymphocytes of exposed nurses compared with the control group (4.36+/-2.23 versus 9.02+/-4.67). The multiple regression analysis revealed a statistically significant relationship (p=0.0009) between MN frequency and exposure status, indicating that the level of exposure was the main factor affecting chromosomal damage. As assessed by FISH analysis, the overall frequencies of centromere-positive MN in the control and exposed groups were 43 and 49%, respectively. The increase observed in the exposed group may suggest a slight, statistically insignificant pro-aneugenic effect of exposure to nitrous oxide.     

The effects of interaction compartments on stability for competitive systems

The interactions between species are unlikely to be randomly arranged, and there is increasing evidence that most interactions occur within small species sub-groups, or compartments, that do not strongly interact with one another. We examine whether arranging the interactions of a competitive system into compartments influences the system properties of linear stability, feasibility, reactivity, and biomass stability, thereby altering the likelihood of species persistence. Model Lotka-Volterra systems of diffuse competition were analysed with interactions arranged randomly and in compartments. It was found, using a variety of dynamical measures, that arranging interactions into compartments enhances the likelihood of species persistence. Since many natural competitive systems appear to have interactions arranged within compartments, this may be an outcome of the positive attributes that this form of organization offers.     

Indiscriminate polyandry and male parental effort

Extrapair paternity involves cooperation between mated females and extrapair males. On the other hand, mated males exhibit a spectrum of anti-cuckolding strategies. Hence, extrapair attributes of diverse species and populations reported in the literature are particular solutions of evolutionary games involving gender-specific cuckolding/anti-cuckolding strategies. Here we use game theoretical methods to study the effect of male paternal effort conserving strategies in situations where females seek extrapair fertilizations (EPF) for reasons of genetic compatibility and/or in pursuit of genetic diversity for their offspring. In such cases, females cannot make a pre-copulatory selection of the optimal genetic partners, and therefore combine promiscuous copulation with the use of in copula and/or post-copulatory selection mechanisms to optimize the genetic endowment of their offspring—indiscriminate polyandry. Our results indicate that, when indiscriminate polygamy is constrained by the availability of extrapair male partners, there are three possible (parameter regime wise) evolutionary stable strategy solutions. (1) All females seek EPF, while all males restrict parental care. (2) All females seek EPF, while all males are unconditionally parental. (3) Females use a combination strategy where pursuit of EPF is mixed—on either a population, or an individual level—with genetic monogamy, while all males use a conditional paternal care strategy, which involves adjusting their parental efforts according to their certainty of paternity.     

The European Renal Genome Project: An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease

Rapid progress in genome research creates a wealth of information on the functional annotation of mammalian genome sequences. However, as we accumulate large amounts of scientific information we are facing problems of how to integrate and relate the data produced by various genomic approaches. Here, we propose the novel concept of an organ atlas where diverse data from expression maps to histological findings to mutant phenotypes can be queried, compared and visualized in the context of a three-dimensional reconstruction of the organ. We will seek proof of concept for the organ atlas by elucidating genetic pathways involved in development and pathophysiology of the kidney. Such a kidney atlas may provide a paradigm for a new systems-biology approach in functional genome research aimed at understanding the genetic bases of organ development, physiology and disease.Key Words: EuReGene, kidney, genome, development, pathophysiology, genetics