Can inverse density dependence at small spatial scales produce dynamic instability in animal populations?

All else being equal, inversely density-dependent (IDD) mortality destabilizes population dynamics. However, stability has not been investigated for cases in which multiple types of density dependence act simultaneously. To determine whether IDD mortality can destabilize populations that are otherwise regulated by directly density-dependent (DDD) mortality, I used scale transition approximations to model populations with IDD mortality at smaller “aggregation” scales and DDD mortality at larger “landscape” scales, a pattern observed in some reef fish and insect populations. I evaluated dynamic stability for a range of demographic parameter values, including the degree of compensation in DDD mortality and the degree of spatial aggregation, which together determine the relative importance of DDD and IDD processes. When aggregation-scale survival was a monotonically increasing function of density (a “dilution” effect), dynamics were stable except for extremely high levels of aggregation combined with either undercompensatory landscape-scale density dependence or certain values of adult fecundity. When aggregation-scale survival was a unimodal function of density (representing both “dilution” and predator “detection” effects), instability occurred with lower levels of aggregation and also depended on the values of fecundity, survivorship, detection effect, and DDD compensation parameters. These results suggest that only in extreme circumstances will IDD mortality destabilize dynamics when DDD mortality is also present, so IDD processes may not affect the stability of many populations in which they are observed. Model results were evaluated in the context of reef fish, but a similar framework may be appropriate for a diverse range of species that experience opposing patterns of density dependence across spatial scales.     

Fitness consequences of anthropogenic hybridization in wild red-legged partridge (Alectoris rufa, Phasianidae) populations

Hybridization is a widespread phenomenon, which plays crucial roles in the speciation of living beings. However, unnatural mixing of historically isolated taxa due to human-related activities has increased in recent decades, favouring levels of hybridization and introgression that can have important implications for conservation. The wild red-legged partridge (Alectoris rufa, Phasianidae) populations have recently declined and the releases of farm-reared partridges have become a widespread management strategy. The native range of the red-legged is limited to the south-west of Europe (from Italy to Portugal). This species does not breed in sympatry with the chukar partridge (A. chukar), whose range is Eurasian (from Turkey to China). However, red-legged partridges have often been hybridized with chukar partridges to increase the productivity of farmed birds, and game releases may have spread hybrid birds into the wild. In this study, we investigated the fitness (survival and breeding) differences between hybrid and “pure” red-legged partridges in a wild population located in central Spain. Incubation probability was similar in hybrids and “pure” partridges. Hybrid females laid larger clutches than “pure” ones, but hatching success did not differ between hybrid and “pure” partridges. Hybrid birds had lower survival rate than “pure” ones, mainly because of higher predation rates. Our results show that, despite lower survival, hybrid partridges breed in natural populations, so this could increase extinction risk of wild pure partridge populations, through releases of farmed hybrid birds. The consequences of continued releases could be of vital importance for the long term conservation of wild red-legged partridges.     

Voiceprint identification and its application to sociological studies of wild Japanese monkeys (Macaca fuscata yakui)

Japanese monkeys often exchange the particular vocal sound, “coo,” especially when they feed or move as a group. It was considered that the “coo” sound had no positive social meaning, perhaps because the “coo” sound network and its function were hidden behind other behavioral observations. For identification of the vocalizer only from hearing the “coo” sound, three phonetic values, i.e., the “fundamental,” “duration,” and “formants,” plus other characteristics were used as indices of voiceprints. The results indicated that these were effective for identifying the vocalizer in two-thirds of the adults in the study troop which was composed of 12 adults and 16 immature members. The “coo” sound exchange network among the troop members (adults) was drawn on the basis of the voiceprint identification. The network showed three characteristics as follows: (1) matriarchs of the kin-groups frequently exchanged “coo” sounds with each other; (2) the other females exchanged “coo” sounds mostly within their own kin-groups; and (3) males seldom participated in the “coo” sound exchange. This suggests that “coo” sound exchange plays a central role for the matriarch of kin-groups in binding each kin-group and, ultimately, in binding all members together into an organized troop.     

Synchrony and Asynchrony for Neuronal Dynamics Defined on Complex Networks

We describe and analyze a model for a stochastic pulse-coupled neuronal network with many sources of randomness: random external input, potential synaptic failure, and random connectivity topologies. We show that different classes of network topologies give rise to qualitatively different types of synchrony: uniform (Erdős–Rényi) and “small-world” networks give rise to synchronization phenomena similar to that in “all-to-all” networks (in which there is a sharp onset of synchrony as coupling is increased); in contrast, in “scale-free” networks the dependence of synchrony on coupling strength is smoother. Moreover, we show that in the uniform and small-world cases, the fine details of the network are not important in determining the synchronization properties; this depends only on the mean connectivity. In contrast, for scale-free networks, the dynamics are significantly affected by the fine details of the network; in particular, they are significantly affected by the local neighborhoods of the “hubs” in the network.     

Reconstruction of Some Hybrid Phylogenetic Networks with Homoplasies from Distances

Suppose G is a phylogenetic network given as a rooted acyclic directed graph. Let X be a subset of the vertex set containing the root, all leaves, and all vertices of outdegree 1. A vertex is “regular” if it has a unique parent, and “hybrid” if it has two parents. Consider the case where each gene is binary. Assume an idealized system of inheritance in which no homoplasies occur at regular vertices, but homoplasies can occur at hybrid vertices. Under our model, the distances between taxa are shown to be described using a system of numbers called “originating weights” and “homoplasy weights.” Assume that the distances are known between all members of X. Sufficient conditions are given such that the graph G and all the originating and homoplasy weights can be reconstructed from the given distances.     

From sepiamelanin to chemical ecology of opisthobranchs and diatoms: an exciting 40 years game in the field of marine natural products

This paper reports the lecture delivered on the occasion of the “Ceremony of Professional Recognition” to the author at the 6th European Conference on Marine Natural Products (Porto, Portugal, 19–23 July 2009). The most recent results obtained studying opisthobranchs and diatoms at ICB are presented after a synthetic overview of the most significant moves played during this exciting 40 years game in the field of Marine Natural Products. In a symbolic manner this career is compared to a chess game. After the “romantic” opening dedicated to the study of natural black (melanin) and red-brown (phaeomelanins) pigments in the prestigious group of Rodolfo A. Nicolaus, the research on marine organisms started in 1969 and rapidly led to the characterization of an impressive number of new compounds exhibiting very unusual structures. Substantially, the “structure hunt” ended with the publication of a series of alkaloids with absolutely unprecedented structural features: the saraines. Slowly, the scientific interest shifted “from structure to function”. Opisthobranchs were selected as models to investigate. The majority of the protective allomones possessed by opisthobranch molluscs are sequestered through the food chain from algae and invertebrates. However, opisthobranchs were also able to biosynthesize many compounds structurally related to typical molecules possessed by their prey. These aspects “from function to ecology, to biosynthesis, to evolution” are discussed in detail.     

Physics,biology, and sociology: A reappraisal

To the extent that all biological phenomena are perceivable only through their physical manifestations, it may be justified to assume that all biological phenomena will be eventually represented in terms of physics; perhaps not of present day physics, but of some “extended” form of it. However, even if this should be correct, it must be kept in mind that representing individual biological phenomena in terms of physics is not the same as deducing from known physical laws the necessity of biological phenomena. Drawing an analogy from pure mathematics, it is possible that while every biological phenomenon may be represented in terms of physics, yet biological statements represent a class of “undecidable” statements within the framework of physics. Such a conjecture is reinforced by the history of physics itself and illustrated on several examples. The 19th century physicists tried in vain todeduce electromagnetic phenomena from mechanical ones. A similar situation may exist in regard to biological and social sciences. Quite generally, the possibility of representing a class B phenomena in terms of class A phenomena does not imply that the phenomena of class B can be deduced from those of class A. The consequences of the above on the relation between physics, biology, and sociology are studied. A tentative postulational formulation of basic biological principles are given and some consequences are discussed. It is pointed out that not only can the study of biological phenomena throw light on some physical phenomena, but that the study of social phenomena may be of value for the understanding of the structures and functions of living organisms. The possibility of a sort of “socionics” is indicated.     

Ecosystem-like behavior of a random-interaction model I

The behavior of large systems of randomly-interacting variables is examined using an intentionally simplified model. The stable positive solutions are found to exhibit to a significant degree some well-known properties of ecological systems. This resemblance (including for example the predominance of “predator-prey” interactions) is all the more striking in view of the lack of biological “data” at the input end. The findings suggest it advisable to distinguish two kinds of properties in ecosystems. One kind would depend on specifically biological mechanisms; the other would characterize a wide class of persistent systems, and arise from the need for a dynamic balance between positive and negative feedback.     

Sexes,species, and genomes: why males and females are not like humans and chimpanzees

This paper describes, analyzes, and critiques the construction of separate “male” and “female” genomes in current human genome research. Comparative genomic work on human sex differences conceives of the sexes as like different species, with different genomes. I argue that this construct is empirically unsound, distortive to research, and ethically questionable. I propose a conceptual model of biological sex that clarifies the distinction between species and sexes as genetic classes. The dynamic interdependence of the sexes makes them “dyadic kinds” that are not like species, which are “individual kinds.” The concept of sex as a “dyadic kind” may be fruitful as a remedy to the tendency to conceive of the sexes as distinct, binary classes in biological research on sex more generally.     

Estimate of complexity of behavioral patterns in ants: analysis of hunting behavior in <Emphasis Type="Italic">Myrmica rubra</Emphasis> (Hymenoptera,Formicidae) as an example

A method for estimating the complexity of behavioral patterns of ants based on the Kolmogorov complexity is considered. Behavioral sequences are presented as “texts” compressed with the KGB Archiver (v. 1.2). The elements of behavior (a total of 10) singled out from video records served as an alphabet. The comparison of “successful” and “incomplete” hunting behaviors in Myrmica rubra showed that successful hunting patterns were characterized by less complexity than “incomplete” ones. It was assumed that complete patterns had less redundancy and better predictability. The smallest complexity was revealed in complete hunting patterns of naive (laboratory reared) ants in comparison with members of a natural colony. In perspective, quantitative evaluation of complexity of behavioral patterns will help to evaluate the level of discrete variability within ant colonies.     

Correlations between the psychological peculiarities of an individual and the efficacy of a single neurofeedback session (by the EEG characteristics)

Modifications of different EEG rhythms induced by a single neurofeedback session (by the EEG characteristics) directed toward an increase in the ratio of the spectral powers (SPs) of the α vs θ oscillations were compared with the psychological characteristics of the tested subjects (the group included 30 persons). A generally accepted neurofeedback technique was used; the intensity of acoustic white noise served as the feedback signal. EEG potentials were recorded from the C3 and C4 leads. Psychological testing was carried out using Eysenck’s (EPQ), Rusalov’s (OST), and (16 PF) questionnaires. The directions of changes in the SPs of EEG frequency components were found to significantly correlate with some individuality-related peculiarities of the tested subjects. The SP of the δ rhythm correlated with the EPQ scale “neuroticism,” OST scale “social plasticity,” and 16 PF factors H (“parmia”), I (“premsia”), and Q₃ (“self-control of behavior”). The SP of the θ component demonstrated correlations with the OST scales “ergisity,” “plasticity,” and “social temp” and with 16 PF factors M (“autia”), Q₄ (“frustration”), and Q1 (“exvia”). The SP of the α rhythm correlated with 16 PF factors Q₃ (“self-control of behavior”), G (“strength of superEgo”), O (“hypothymia”), L (“protension”), and N (“shrewdness”). The SP of the β rhythm correlated with the OST scale “emotionality,” while that of the γ rhythm showed correlations with the 16 PF indices L (“protension”) and M (“autia”). Changes in the ratio of the α vs θ SPs correlated with the EPQ scale “neuroticism.” Thus, our data confirm the statement that a high individual variability of the results of a single (first in the series) neurofeedback session is to a great extent related to peculiarities of the individual psychological pattern of the subject. Neirofiziologiya/Neurophysiology, Vol. 38, No. 3, pp. 239–247, May–June, 2006.     

Developing Microsatellite Multiplex and Megaplex PCR Systems for High-Throughput Characterization of Breeding Progenies and Linkage Maps Spanning the Apricot (<Emphasis Type="Italic">Prunus armeciaca</Emphasis> L.) Genome

One hundred and twenty apricot and peach simple sequence repeat (SSR) markers have been used in the molecular characterization of a BC1 apricot progeny of 73 seedlings derived from the cross between the F1 selection “Z506-07” (“Orange Red” × “Currot”) and the Spanish cultivar “Currot.” To reduce costs and improve the capacity of molecular characterization assays using SSR markers, a series of seven megaplex PCRs containing between six and 20 SSR markers were developed for the molecular characterization of the apricot breeding progeny studied. Amplification was successful in apricot progenitors and in the progeny with 114 of the 120 (95%) SSR markers with a suitable level of polymorphism (1.7 alleles/marker) detected in the BC1 descendants studied. In addition, the implementation of megaplex PCR increased the efficiency and reduced the cost of this type of molecular studies. The implications of these results for apricot-breeding programs and the construction of genetic linkage maps have been also discussed.     

The Biodiversity Discourse: Categorisation of Indigenous People in a Mexican Bio-prospecting Case

Indigenous knowledge is often portrayed as static and traditional, while indigenous people are considered victims of exploitation. In the name of development and empowerment NGOs as well as scientists may run the risk of representing indigenous communities that fit their definition of the “correct” way to be indigenous. However, for indigenous people knowledge is not necessarily a static condition in a binary position to science or the ‘modern’ world. Rather, it is a dynamic condition that draws from experience and adapts to a changing environment. The perspective advanced in this paper is that all forms of knowledge, including indigenous knowledge(s), are situated and hybrid. Our argument draws from research carried out in Chiapas, Mexico, regarding the ICBG-Maya bio-prospecting project that was initiated in the 1990s and later terminated due to accusations of bio-piracy.     

Inheritance of resistance to Plum pox virus in apricot (Prunus armeniaca L.)

The inheritance of resistance to Plum pox virus (PPV) has been studied in 1,178 apricot hybrids. Seven hundred and eighteen F1 hybrids, obtained from controlled crosses between the susceptible Greek cultivar “Bebecou” and the resistant PPV cultivars of American origin (“Stark Early Orange,” ‘NJA2,” ‘Veecot,” “Sunglo,” “Harlayne,” and “Orangered”) were evaluated for resistance to the PPV-M (Marcus) strain, 8 years after artificial inoculation. The inheritance of resistance to PPV has been additionally studied for the first time in a BC₁ population of 95 apricot hybrids for four vegetative periods. Reaction of each hybrid to PPV-M was scored through visual symptoms, indexing onto GF-305 and double-antibody sandwich enzyme-linked immunosorbent assay tests. Segregation within the hybrids, determined by Chi-squared analysis, fits a 1:1 ratio (P ≤ 0.05) of the resistant vs susceptible, indicating that resistance to PPV is controlled by a single dominant gene locus and that the above six resistant cultivars are heterozygous for the trait. Plants carrying this gene may initially develop disease symptoms on leaves but eventually recover and no virus can be detected in leaves. Susceptible plants show similar symptoms initially but remain symptomatic. Inheritance of resistance to PPV also has been studied in 365 F1 hybrids by crossing the resistant cultivar “Stella” with the susceptible “Bebecou” and the resistant cultivars “Sunglo” and “NJA2,” for 8 years after inoculation. The segregation ratio was 1:0 (resistant/susceptible) suggesting that “Stella” is homozygous for the resistance trait. The purpose of this work was the enhancement of the knowledge of inheritance of resistance to PPV for the selection of new cultivars.     

Assessment of Gene Flow from Genetically Modified Anthracnose-Resistant Chili Pepper (Capsicum annuum L.) to a Conventional Crop

We conducted a 2-year field assessment of the gene flow from genetically modified (GM) chili pepper (Capsicum annuum L.), containing the PepEST (pepper esterase) gene, to a non-GM control line “WT512” and two commercial hybrid cultivars, “Manidda” and “Cheongpung Myeongwol (CM).” After seeds were collected from the pollen-recipient non-GM plants, hybrids between them and the GM peppers were screened by a hygromycin assay. PCR with the targeting hpt gene was performed to confirm the presence of transgenes in hygromycin-resistant seedlings. Out of 7,071 “WT512” seeds and 6,854 “Manidda” seeds collected in 2006, eight and 12 hybrids, respectively, were detected. In 2007, 33 hybrids from 3,456 “WT512” seeds and 50 hybrids from 3,457 “CM” seeds were found. The highest frequency of gene flow, 6.19%, was observed in that 2007 trial. These results suggest that a limited isolation distance would be sufficient to prevent gene flow from GM to conventionally bred chili peppers.     

Circumscription of Malvaceae (Malvales) as determined by a preliminary cladistic analysis of morphological, anatomical, palynological, and chemical characters

We report a phylogenetic analysis of “core” Malvales (Tiliaceae, Sterculiaceae, Bombacaceae, and Malvaceae) based on morphological, anatomical, palynological, and chemical features. The results of the analyses lead to the conclusion that Tiliaceae, Sterculiaceae, and Bombacaceae, as variously delimited, are paraphyletic; only the Malvaceae are likely monophyletic. The genera of “core” Malvales form a well-defined clade. Genera of “Tiliaceae” constitute the basal complex within “core” Malvales. The “Sterculiaceae” (most genera)+ “Bombacaceae” + Malvaceae form a clade on the basis of a monadelphous androecium; “Bombacaceae”+ Malvaceae also form a clade, which is diagnosable on the basis of monoloculate anthers. It is clear that the traditional classification, with its arbitrarily delimited evolutionary grades, is unsatisfactory, especially if one seeks to reflect phylogeny accurately. Thus, Malvaceae is redefined to refer to the most recent common ancestor of plants previously considered to be “Tiliaceae,” “Sterculiaceae,” “Bombacaceae,” and Malvaceae, and all of the descendants of that ancestor. This broadly circumscribed Malvaceae can be diagnosed by several presumed synapomorphies, but we draw special attention to the unusual floral nectaries that are composed of densely packed, multicellular, glandular hairs on the sepals (or less commonly on the petals or androgynophore).     

Biotechnology of β-adrenergic receptors

The emergence of Biotechnology has provided pharmacologists with a variety of methods for investigating the structure, the function, and the regulation of membrane-bound receptors with a precision that was not imagined even five years ago. These new tools have been developed and used to analyze the known catecholamine β₁- and β₂ receptors and to discover and study a new subtype, the β-adrenergic receptor. We review here the salient features of each of these three receptors, compare their structural and functional properties, and propose models to explain their differential regulation in time and space. A whole family of proteins has now been found to share with the β-adrenergic receptors their most prominent features, including seven transmembrane domains and coupling with GTP-binding “G” proteins. We therefore propose that the biotechnology-based procedures developed for the β-adrenergic receptors will be well applicable to the other members of this “R₇G” family of receptors.     

The Rise of Modern Humans

Human beings are distinguished most strikingly by their unique “symbolic” way of processing information about the world. Although based on a long evolutionary history, the modern human cognitive style is not predicted by that history. It is not the product of a process of incremental refinement but is instead “emergent,” representing an entirely distinct level of complexity. Physically, Homo sapiens is very distinctive, its peculiarities clearly resulting from a significant developmental reorganization with numerous skeletal ramifications and quite plausibly others as well. It seems reasonable to suppose that the structural underpinnings of symbolic thought were acquired in this reorganization. Still, the fossil and archaeological records indicate that the first anatomically recognizable members of the species predated the first humans who behaved in a demonstrably symbolic manner. So while the biological potential for symbolic thinking most likely arose in the morphogenetic event that gave rise to H. sapiens as a distinctive anatomical entity, this new capacity was evidently exaptive, in the sense that it had to await its “discovery” and expression, clearly through a cultural stimulus that was plausibly the invention of language. One manifestation of symbolic reasoning is the adoption of technological change in response to environmental challenges, in contrast to earlier responses that typically used existing technologies in new ways. As climates changed at the end of the last Ice Age, this new technophile proclivity was expressed in a shift toward agriculture and sedentary lifestyles, precipitating a fundamentally new (and potentially self-destructive) relationship with Nature. Both of the two most radical and fateful evolutionary innovations in the history of life (symbolic thinking and sedentary lifestyles) were thus very recent occurrences, well within the short tenure of H. sapiens.     

Unreasonable implications of reasonable idiotypic network assumptions

We first analyse a simple symmetric model of the idiotypic network. In the model idiotypic interactions regulate B cell proliferation. Three non-idiotypic processes are incorporated: (1) influx of newborn cells; (2) turnover of cells: (3) antigen. Antigen also regulates proliferation. A model of 2 B cell populations has 3 stable equilibria: one virgin, two immune. The twodimensional system thus remembers antigens, i.e. accounts for immunity. By contrast, if an idiotypic clone proliferates (in response to antigen), its anti-idiotypic partner is unable to control this. Symmetric idiotypic networks thus fail to account for proliferation regulation. In high-D networks we run into two problems. Firstly, if the network accounts for memory, idiotypic activation always propagates very deeply into the network. This is very unrealistic, but is an implication of the “realistic” assumption that it should be easier to activate all cells of a small virgin clone than to maintain the activation of all cells of a large (immune) clone. Secondly, graph theory teaches us that if the (random) network connectance exceeds a threshold level of one interaction per clone, most clones are interconnected. We show that this theory is also applicable to immune networks based on complementary matching idiotypes. The combination of the first “percolation” result with the “interconnectancr” result means that the first stimulation of the network with antigen should eventually affect most of the clones. We think this is unreasonable. Another threshold property of the network connectivity is the existence of a virgin state. A gradual increase in network connectance eliminates the virgin state and thus causes an abrupt change in network behaviour. In contrast to weakly connected systems, highly connected networks display autonomous activity and are unresponsive to external antigens. Similar differences between neonatal and adult networks have been described by experimentalists. The robustness of these results is tested with a network in which idiotypic inactivation of a clone occurs more generally than activation. Such “long-range inhibition” is known to promote pattern formation. However, in our model it fails to reduce the percolation, and additionally, generates semi-chaotic behaviour. In our network, the inhibition of a clone that is inhibiting can alter this clone into a clone that is activating. Hence “long-range inhibition” implies “long-range activation”, and idiotypic activation fails to remain localized. We next complicate this model by incorporating antibody production. Although this “antibody” model statically accounts for the same set of equilibrium points, it dynamically fails to account for state switching (i.e. memory). The switching behaviour is disturbed by the autonomous slow decay of the (long-lived) antibodies. After antigenic triggering the system now performs complex cyclic behaviour. Finally, it is suggested that (idiotypic) formation of antibody complexes can play only a secondary role in the network. In conclusion, our results cast doubt on the functional role of a profound idiotypic network. The network fails to account for proliferation regulation, and if it accounts for memory phenomena, it “explodes” upon the first encounter with antigen due to extensive percolation.