Chemistry and biodiversity

Complex structures produced by noncatalyzed multi-step chemical processes must have highly probable origins and assembly routes. Within any frame of reference, life is easily the most-complex self-assembled structure known to man. It is not possible to calculate a finite time for biogenesis by statistical mechanics, but the abundance of life makes it reasonable to propose an accelerating principle of nature that naturally shortened the time for cell formation to a billion years or less. This hypothetical principle, which I have called valence-orbital bias, is thought to be responsible for the discrepancy between statistics and observation, and carries with it, as a conditio sine qua non, multiple origins of life.The new concept resolves the differences between the predictions based on statistical mechanics and the relatively rapid appearance of life during the post-accretion period. It suggests as well that species and variants, the units of propagation, may also have been the units of evolution. Produced in profusion by chemistry, the origins are culled by natural selection, whereby failure means extinction, not adaptation. Biodiversity, thus, becomes a direct consequence of chemistry without positive feedback from the environment and without a constructive role for mutation.     

The origins of gestures and language: history,current advances and proposed theories

Investigating in depth the mechanisms underlying human and non‐human primate intentional communication systems (involving gestures, vocalisations, facial expressions and eye behaviours) can shed light on the evolutionary roots of language. Reports on non‐human primates, particularly great apes, suggest that gestural communication would have been a crucial prerequisite for the emergence of language, mainly based on the evidence of large communication repertoires and their associated multifaceted nature of intentionality that are key properties of language. Such research fuels important debates on the origins of gestures and language. We review here three non‐mutually exclusive processes that can explain mainly great apes' gestural acquisition and development: phylogenetic ritualisation, ontogenetic ritualisation, and learning via social negotiation. We hypothesise the following scenario for the evolutionary origins of gestures: gestures would have appeared gradually through evolution via signal ritualisation following the principle of derived activities, with the key involvement of emotional expression and processing. The increasing level of complexity of socioecological lifestyles and associated daily manipulative activities might then have enabled the acquisition and development of different interactional strategies throughout the life cycle. Many studies support a multimodal origin of language. However, we stress that the origins of language are not only multimodal, but more broadly multicausal. We propose a multicausal theory of language origins which better explains current findings. It postulates that primates' communicative signalling is a complex trait continually shaped by a cost–benefit trade‐off of signal production and processing of interactants in relation to four closely interlinked categories of evolutionary and life cycle factors: species, individual and context‐related characteristics as well as behaviour and its characteristics. We conclude by suggesting directions for future research to improve our understanding of the evolutionary roots of gestures and language.     

Detection of Macromolecular Fractions in HCN Polymers Using Electrophoretic and Ultrafiltration Techniques

Elucidating the origin of life involves synthetic as well as analytical challenges. Herein, for the first time, we describe the use of gel electrophoresis and ultrafiltration to fractionate HCN polymers. Since the first prebiotic synthesis of adenine by Oró, HCN polymers have gained much interest in studies on the origins of life due to the identification of biomonomers and related compounds within them. Here, we demonstrate that macromolecular fractions with electrophoretic mobility can also be detected within HCN polymers. The migration of polymers under the influence of an electric field depends not only on their sizes (one‐dimensional electrophoresis) but also their different isoelectric points (two‐dimensional electrophoresis, 2‐DE). The same behaviour was observed for several macromolecular fractions detected in HCN polymers. Macromolecular fractions with apparent molecular weights as high as 250 kDa were detected by tricine‐SDS gel electrophoresis. Cationic macromolecular fractions with apparent molecular weights as high as 140 kDa were also detected by 2‐DE. The HCN polymers synthesized were fractionated by ultrafiltration. As a result, the molecular weight distributions of the macromolecular fractions detected in the HCN polymers directly depended on the synthetic conditions used to produce these polymers. The implications of these results for prebiotic chemistry will be discussed.     

Interpreting the Role of Climbing in Primate Locomotor Evolution: Are the Biomechanics of Climbing Influenced by Habitual Substrate Use and Anatomy?

Vertical climbing is widely accepted to have played an important role in the origins of both primate locomotion and of human bipedalism. Yet, only a few researchers have compared climbing mechanics in quadrupedal primates that vary in their degree of arboreality. It is assumed that primates using vertical climbing with a relatively high frequency will have morphological and behavioral specializations that facilitate efficient climbing mechanics. We test this assumption by examining whether time spent habitually engaged in climbing influences locomotor parameters such as footfall sequence, peak forces, and joint excursions during vertical climbing. Previous studies have shown that during climbing, the pronograde and semiterrestrial Macaca fuscata differs in these parameters compared to the more arboreal and highly specialized, antipronograde Ateles geoffroyi. Here, we examine whether a fully arboreal, quadrupedal primate that does not regularly arm-swing will exhibit gait and force distribution patterns intermediate between those of Macaca fuscata and Ateles geoffroyi. We collected footfall sequence, limb peak vertical forces, and 3D hindlimb excursion data for Macaca fascicularis during climbing on a stationary pole instrumented with a force transducer. Results show that footfall sequences are similar between macaque species, whereas peak force distributions and hindlimb excursions for Macaca fascicularis are intermediate between values reported for M. fuscata and Ateles geoffroyi. These results support the notion that time spent climbing is reflected in climbing mechanics, even though morphology may not provide for efficient mechanics, and highlight the important role of arboreal locomotor activity in determining the pathways of primate locomotor evolution.     

Statistical correlation between enterovirus genome copy numbers and infectious viral particles in wastewater samples

Aims: Classic virological tests are time consuming and labour‐intensive; real‐time RT‐PCR has proven to be a fast method to detect and quantify enterovirus genomes in clinical and environmental samples. This method is unable to discriminate between infective and noninfective enterovirus particles; few clinical studies have compared real‐time RT‐PCR and viral culture. We wondered if the enterovirus genome quantification could be correlated to the infectivity. Methods and Results: We used the statistical approach to verify our hypotheses to correlate data, obtained by the standard method (most probable number of cytopathic units—MPNCU) and molecular test (real‐time RT‐PCR), on wastewater treatment plant samples. Chi‐squared test was used, considering several cut‐off values (‘50’‐‘100’‐‘200’ genome copy numbers), to determine statistical significance in comparison of the two methods. Chi‐square value was not significant when cut‐off of 50 (P = 0·103) and 100 (P = 0·178) was assumed but was significant with cut‐off of 200 (P = 0·044). Conclusion: This limit, 200 genome copy, could be used as cut‐off value to indicate enterovirus survival in environmental monitoring. Significant and Impact of the Study: To introduce a fast procedure that is able to compensate for disadvantages of cell culture method for viral environmental analyses.     

Towards a General Definition of Life

A new definition of life is proposed and discussed in the present article. It is formulated by modifying and extending NASA’s working definition of life, which postulates that life is a “self-sustaining chemical system capable of Darwinian evolution”. The new definition includes a thermodynamical aspect of life as a far from equilibrium system and considers the flow of information from the environment to the living system. In our derivation of the definition of life we have assumed the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. The new proposed definition of life is independent of the mode of evolution, regardless of whether Lamarckian or Darwinian evolution operated at the origins of life and throughout evolutionary history. The new definition of life presented herein is formulated in a minimal manner and it is general enough that it does not distinguish between individual (metabolic) network and the collective (ecological) one. The newly proposed definition of life may be of interest for astrobiology, research into the origins of life or for efforts to produce synthetic or artificial life, and it furthermore may also have implications in the cognitive and computer sciences.

     

The influence of local environment on the aging and mortality ofAedes aegypti (L.): Case study in Fortaleza‐CE,Brazil

It is generally assumed that the daily probability of survival of mosquitoes is independent of age. To test this assumption we have conducted a three‐year experimental fieldwork study (2005–2007) at Fortaleza‐CE in Brazil, determining daily survival rates of the dengue vector Aedes aegypti (L.). Survival rates of adult Ae. aegypti may be age‐dependent and the statistical analysis is a sensitive approach for comparing patterns of mosquito survival. The mosquito survival data were better fit by a Weibull survival function than by the more traditionally used Gompertz or logistic survival functions. Gompertz, Weibull, or logistic survival functions often fit the survival, and the tails of the survival curves usually appear to fall between the values predicted by the three functions. We corroborate that the mortality of Ae. aegypti in semi‐natural conditions may no more be considered as a constant phenomenon during the life of adult mosquitoes but varies according to the age and environmental conditions under a tropical climate. This study estimates the variability in the survival rate of Ae. aegypti and environmental factors that are related to such variability. The statistical analysis shows that the fitting ability, concerning the hazard function, was in decreasing order: Seasonal Cox, the three‐parameter Gompertz, and the three‐parameter Weibull, that was similar to the three‐parameter logistic. The advantage of using the Cox model is that it is convenient for exploring the relationship between survival and several explanatory variables. The Cox model has the advantage of preserving the variable in its original quantitative form and of using a maximum of information. The survival analyses indicate that mosquito mortality is both age‐ and environment‐dependent.     

Evidence for long‐term change in length,mass and migration phenology of anadromous spawners in French Atlantic salmon Salmo salar

This study provides new data on Atlantic salmon Salmo salar life‐history traits across France. Using a long‐term recreational angling database (1987–2013) covering 34 rivers in three regions (genetic units), a decline in individual length, mass and a delayed adult return to French rivers was reported. Temporal similarities in trait variations between regions may be attributed to common change in environmental conditions at sea. The relative rate of change in phenotypic traits was more pronounced in early maturing fish [1 sea‐winter (1SW) fish] than in late maturing fish (2SW fish). Such contrasted response within populations highlights the need to account for the diversity in life histories when exploring mechanisms of phenotypic change in S. salar. Such detailed life‐history data on returning S. salar have not previously been reported from France. This study on French populations also contributes to reducing the gap in knowledge by providing further empirical evidence of a global pattern in S. salar across its distribution range. Results are consistent with the hypothesis that the observed changes in life‐history traits are primarily associated with environmental changes in the North Atlantic Ocean. They also emphasize the presence of less important, but still significant contrasts between region and life history.     

Complexity, Self-Organization and Selection

Recent work on self organization promises an explanation of complex order which is independent of adaptation. Self-organizing systems are complex systems of simple units, projecting order as a consequence of localized and generally nonlinear interactions between these units. Stuart Kauffman offers one variation on the theme of self-organization, offering what he calls a ``statistical mechanics' for complex systems. This paper explores the explanatory strategies deployed in this ``statistical mechanics,' initially focusing on the autonomy of statistical explanation as it applies in evolutionary settings and then turning to Kauffman's analysis. Two primary morals emerge as a consequence of this examination: first, the view that adaptation and self-organization should be seen as competing theories or models is misleading and simplistic; and second, while we need a synthesis treating self-organization and adaptation as geared toward different problems, at different levels of organization, and deploying different methods, we do not yet have such a synthesis.     

Birth,survival and differentiation of neurons in an adult crustacean brain

Life‐long neurogenesis is a characteristic feature of many vertebrate and invertebrate species. In decapod crustaceans, new neurons are added throughout life to two cell clusters containing local (cluster 9) and projection (cluster 10) interneurons in the olfactory pathway. Adult‐born neurons in clusters 9 and 10 in crayfish have the anatomical properties and chemistry of mature neurons by 6 months after birth. Here we use 5‐bromo‐2′‐deoxyuridine (BrdU) incorporation to pulse label mitotically active cells in these cell clusters, followed by a survival time of up to 8 months, during which crayfish (Cherax destructor) were sacrificed at intervals and the numbers of BrdU‐labeled cells quantified. We find a decrease in the numbers of BrdU‐labeled cells in cell cluster 10 between the first and second weeks following BrdU exposure, suggesting a period of cell death shortly after proliferation. Additional delayed cell divisions in both cell clusters are indicated by increases in labeled cells long after the BrdU clearing time. The differentiation time of these cells into neurons was defined by detection of the first immunoreactivity for the transmitter SIFamide in cluster 10 BrdU‐labeled cells, which begins at 4 weeks after BrdU labeling; the numbers of SIFamide‐labeled cells continues to increase over the following month. Experiments testing whether proliferation and survival of Cluster 10 cells are influenced by locomotor activity provided no evidence of a correlation between activity levels and cell proliferation, but suggest a strong influence of locomotor activity on cell survival. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 74: 602–615, 2014     

Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera,Podarcis pityusensis (Squamata: Lacertidae)

Two monophyletic sister species of wall lizards inhabit the two main groups of Balearic Islands: Podarcis lilfordi from islets and small islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza, Formentera and associated islets. Genetic diversity within the endangered P. lilfordi has been well characterized, but P. pityusensis has not been studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were analysed from P. pityusensis populations from across its natural range. Two main genetic groupings were identified, although geographical structuring differed slightly between the mtDNA and the nuclear loci. In general, individuals from islets/islands adjacent to the main island of Ibiza were genetically distinct from those from Formentera and the associated Freus islands for both mtDNA and the nuclear loci. However, most individuals from the island of Ibiza were grouped with neighbouring islets/islands for nuclear loci, but with Formentera and Freus islands for the mitochondrial locus. A time‐calibrated Bayesian tree was constructed for the principal mitochondrial lineages within the Balearics, using the multispecies coalescent model, and provided statistical support for divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This suggests a mid‐late Pleistocene intraspecific divergence, compared with an early Pleistocene divergence in P. lilfordi, and postdates some major increases in sea level between 0.4 and 0.6 Ma, which may have flooded Formentera. The program IMa2 provided a posterior divergence time of 0.089–0.221 Ma, which was similar to the multispecies coalescent tree estimate. More significantly, it indicated low but asymmetric effective gene copy migration rates, with higher migration from Formentera to Ibiza populations. Our findings suggest that much of the present‐day diversity may have originated from a late Pleistocene colonization of one island group from the other, followed by allopatric divergence of these populations. Subsequent gene flow between these insular groups seems likely to be explained by recent human introductions. Two evolutionary significant units can be defined for P. pityusensis but these units would need to exclude the populations that have been the subjects of recent admixture.     

A new hypothesis for molecular behavior

In order to understand the living cell, biologists need workable explanations of molecular phenomena. From data in the literature, it is possible to construct a mathematical hypothesis: molecular behavior in the continuum can be represented by a set of simple, logarithmic functions. These functions apply not only to biology, but also to chemistry and to physics.Although empirical in its origins, this hypothesis satisfies criteria which are often associated with good theories. It is comprehensive in its application, and it is mathematically simple. It is easily tested; and it is accurate, when tested. Because it can be correlated with classical atomic and molecular theory, the hypothesis can be used to make strong predictions. The proposal also appears to be consistent with quantum mechanics.     

G4 motifs affect origin positioning and efficiency in two vertebrate replicators

DNA replication ensures the accurate duplication of the genome at each cell cycle. It begins at specific sites called replication origins. Genome‐wide studies in vertebrates have recently identified a consensus G‐rich motif potentially able to form G‐quadruplexes (G4) in most replication origins. However, there is no experimental evidence to demonstrate that G4 are actually required for replication initiation. We show here, with two model origins, that G4 motifs are required for replication initiation. Two G4 motifs cooperate in one of our model origins. The other contains only one critical G4, and its orientation determines the precise position of the replication start site. Point mutations affecting the stability of this G4 in vitro also impair origin function. Finally, this G4 is not sufficient for origin activity and must cooperate with a 200‐bp cis‐regulatory element. In conclusion, our study strongly supports the predicted essential role of G4 in replication initiation.     

Extended larval development time for aphid parasitoids in the presence of plant endosymbionts

Abstract 1. Variation in plant chemistry does not only mediate interactions between plants and herbivores but also those between herbivores and their natural enemies, and plants and natural enemies. 2. Endophytic fungi complete their whole life cycle within the host plant’s tissue and are associated with a large diversity of plant species. Endophytes of the genus Neotyphodium alter the chemistry of the host plant by producing herbivore toxic alkaloids. 3. Here we asked whether the endophyte‐tolerant aphid species Metopolophium festucae could be defended against its parasitoid Aphidius ervi when feeding on endophyte‐infected plants. In a laboratory experiment, we compared life‐history traits of A. ervi when exposed to hosts on endophyte‐infected or endophyte‐free Lolium perenne. 4. The presence of endophytes significantly increased larval and pupal development times, but did not affect the mortality of immature parasitoids or the longevity of the adults. Although the number of parasitoid mummies tended to be reduced on endophyte‐infected plants, the number of emerging parasitoids did not differ significantly between the two treatments. 5. This shows that the metabolism of individual aphids feeding on infected plants may be changed and help in the defence against parasitoids. An increase in parasitoid development time should ultimately reduce the population growth of A. ervi. Therefore, endophyte presence may represent an advantage for endophyte‐tolerant aphid species through extended parasitoid development and its effect on parasitoid population dynamics.     

Recruitment rates exhibit high elasticity and high temporal variation in populations of a short-lived perennial herb

Empirical studies for different life histories have shown an inverse relationship between elasticity (i.e. the proportional contribution to population growth rate) and temporal variation in vital rates. It is accepted that this relationship indicates the effect of selective pressures in reducing variation in those life‐history traits with a major impact on fitness. In this paper, we sought to determine whether changes in environmental conditions affect the relationship between elasticity of vital rates and their temporal variation, and whether vital rates with simultaneously large elasticity and temporal variation might represent a characteristic life‐history strategy. We used demographic data on 13 populations of the short‐lived Hypericum cumulicola over 5–6 years, in three time‐since‐fire classes. For each population of each time‐since‐fire, we computed the mean matrix over years and its respective elasticity matrix, and the coefficients of variation in matrix entries over study years as an estimate of temporal variability. We found that mean elasticity negatively significantly correlated with temporal variation in vital rates in populations (overall eight out of 13) included in each time‐since‐fire. However, seedling recruitment exhibited both high elasticity and high temporal variation in almost all study populations. These results indicated that (1) the general relationship between elasticity and temporal variation in vital rates was not modified by environmental changes due to time‐since‐fire, and (2) high elasticity and high temporal variation in seedling recruitment in H. cumulicola is a particular trait of the species' life history. After seed survival in the soil seed bank, seedling recruitment represents the most important life‐history trait influencing H. cumulicola population growth rate (and fitness). The high temporal variability in seedling recruitment suggests that this trait is determined by environmental cues, leading to an increase in population size and subsequent replenishment of the seed bank in favorable years.     

A Research Proposal on the Origin Of Life. Closing Lecture given at the ISSOL Congress in Oaxaca,Mexico, on July 4, 2002

This paper describes some experiments the author would haveliked to carry out if he had started earlier in the origin-of-life field.The proposal is preceded by a hypothetical outline of the mainevents in the origin of life. According to this outline, the emergence oflife amounts to the transition between two kinds of chemistry: 1) cosmic chemistry, which is beginning to be understood and mostlikely provided the building blocks with which life was first constructed; and 2)biochemistry, the well-known set of enzyme-catalyzedmetabolic reactions that support all living organisms today and must havesupported the universal common ancestor, or LUCA, from which all known formsof life are derived. The pathway leading from one to the other of thosetwo chemistries may be divided into three stages, defined as the pre-RNA, RNA, and protein-DNA stages. A briefsummary of the events that may have occurred in these three stages and ofthe possible underlying mechanisms is given. It is emphasized that theseevents were chemical in nature and, especially, that theymust have prefigured present-day biochemical processes. Protometabolismand metabolism, it is argued, must have been congruent. With congruence as the underlying working hypothesis, threeproblems open to experimental investigation are considered: 1) the involvementof peptides and other multimers as catalysts of early biogenic chemistry;2) the participation of thioesters in primitive energy transactions;and 3) the influence of amino acids on the molecular selection of RNAmolecules.     

Ontogeny of the Furongian (late Cambrian) trilobite Proceratopyge cf. P. Lata Whitehouse from northern Victoria Land,Antarctica, and the evolution of metamorphosis in trilobites

There were multiple origins of metamorphosis‐undergoing protaspides in trilobite evolution: within the superfamilies Remopleuridioidea, Trinucleoidea, and within the Order Asaphida. Recent studies have revealed that the protaspides of the Cambrian representatives of the Remopleuridioidea and the Trinucleoidea did not undergo metamorphosis. However, ontogeny of the Cambrian members of the Order Asaphida has remained unknown. This study documents the ontogeny of the Furongian asaphoidean ceratopygid trilobite, Proceratopyge cf. P. lata Whitehouse, from northern Victoria Land, Antarctica. Two stages for the protaspid phase, five developmental stages for the post‐protaspid cranidia, and ten stages for the post‐protaspid pygidia have been identified. Interestingly, the protaspis directly developed into a meraspis without metamorphosis. A new cladistic analysis resulted in a single most parsimonious tree, according to which the presence of the bulbous commutavi protaspis turns out to be a synapomorphy for Asaphidae + Cyclopygoidea, not a synapomorphy for the Order Asaphida as previously suggested. In addition, it is inferred that there was convergent evolution of indirectly‐developing commutavi protaspides during the Furongian and Early Ordovician. Metamorphosis‐entailing planktonic larvae evolved in many different metazoan lineages near the Cambrian–Ordovician transition, due to the escalating ecological pressure of the Great Ordovician Biodiversification Event. Since the bulbous commutavi protaspid morphology is thought to be an adaptation for a planktonic life mode, the convergent evolution of the indirect development in the three trilobite lineages at this period might have been a result of adaptation to the early phase of the Great Ordovician Biodiversification Event.     

Retired flies,hidden plateaus,and the evolution of senescence in Drosophila melanogaster

Late‐life plateaus in age‐specific mortality have been an evolutionary and biodemographic puzzle for decades. Although classic theory on the evolution of senescence predicts late‐life walls of death, observations in experimental organisms document the opposite trend: a slowing in the rate of increase of mortality at advanced ages. Here, I analyze published life‐history data on individual Drosophila melanogaster females and argue for a fundamental change in our understanding of mortality in this important model system. Mortality plateaus are not, as widely assumed, exclusive to late life, and are not explained by population heterogeneity—they are intimately connected to individual fecundity. Female flies begin adult life in the working stage, a period of active oviposition and low but accelerating mortality. Later they transition to the retired stage, a terminal period characterized by limited fecundity and relatively constant mortality. Because ages of transition differ between flies, age‐synchronized cohorts contain a mix of working and retired flies. Early‐ and mid‐life plateaus are obscured by the presence of working flies, but can be detected when cohorts are stratified by retirement status. Stage‐specificity may be an important component of Drosophila life‐history evolution.     

Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life

Large deposits of montmorillonite are present on the Earth today and it is believed to have been present at the time of the origin of life and has recently been detected on Mars. It is formed by aqueous weathering of volcanic ash. It catalyses the formation of oligomers of RNA that contain monomer units from 2 to 30-50. Oligomers of this length are formed because this catalyst controls the structure of the oligomers formed and does not generate all possible isomers. Evidence of sequence-, regio- and homochiral selectivity in these oligomers has been obtained. Postulates on the role of selective versus specific catalysts on the origins of life are discussed. An introduction to the origin of life is given with an emphasis on reaction conditions based on the recent data obtained from zircons 4.0-4.5Ga.     

Behaviour in a standardized assay,but not metabolic or growth rate,predicts behavioural variation in an adult aquatic top predator Esox lucius in the wild

This study tested for links among behaviour, state and life‐history variables as predicted by the pace‐of‐life hypothesis in adult pike Esox lucius. First, a standardized open‐field behavioural assay was developed to assess individual behaviour of wild‐captured adult E. lucius. Behaviour within the standardized assay predicted swimming behaviour in the lake, providing an ecological validation of the assay. There was no relationship between standardized behaviour and any of the life‐history and state variables, including metabolism, body condition, juvenile growth rate and adult growth rate in contrast to predictions from the pace‐of‐life hypothesis. This study demonstrates that it is possible to assess ecologically relevant behavioural variation in a large‐bodied top predator using a standard open‐field assay, but it is noteworthy that this standardized behaviour is not systematically related to standard metabolism or growth.