Intensive Farming: Evolutionary Implications for Parasites and Pathogens

An increasing number of scientists have recently raised concerns about the threat posed by human intervention on the evolution of parasites and disease agents. New parasites (including pathogens) keep emerging and parasites which previously were considered to be 'under control' are re-emerging, sometimes in highly virulent forms. This re-emergence may be parasite evolution, driven by human activity, including ecological changes related to modern agricultural practices. Intensive farming creates conditions for parasite growth and transmission drastically different from what parasites experience in wild host populations and may therefore alter selection on various traits, such as life-history traits and virulence. Although recent epidemic outbreaks highlight the risks associated with intensive farming practices, most work has focused on reducing the short-term economic losses imposed by parasites, such as application of chemotherapy. Most of the research on parasite evolution has been conducted using laboratory model systems, often unrelated to economically important systems. Here, we review the possible evolutionary consequences of intensive farming by relating current knowledge of the evolution of parasite life-history and virulence with specific conditions experienced by parasites on farms. We show that intensive farming practices are likely to select for fast-growing, early-transmitted, and hence probably more virulent parasites. As an illustration, we consider the case of the fish farming industry, a branch of intensive farming which has dramatically expanded recently and present evidence that supports the idea that intensive farming conditions increase parasite virulence. We suggest that more studies should focus on the impact of intensive farming on parasite evolution in order to build currently lacking, but necessary bridges between academia and decision-makers.     

Implications of clonality for ageing research

Senescence, an organismal performance decline with age, has historically been considered a universal phenomenon by evolutionary biologists and zoologist. Yet, increasing fertility and survival with age are nothing new to plant ecologists, among whom it is common knowledge that senescence is not universal. Recently, these two realities have come into a confrontation, begging for the rephrasing of the classical question that has led ageing research for decades: “why do we senesce?” to a more practical “what are the mechanisms by which some organisms escape from senescence?” Plants are amenable to examining this question because of their rich repertoire of life history strategies. These include the existence of permanent seed banks, vegetative dormancy and ability to produce clones, among others. Here, I use a large number of high resolution demographic models from 181 species that reflect life history strategies and their trade-offs among herbaceous perennials, succulents and shrubs measured under field conditions worldwide to examine whether senescence rates of ramets from clonal plants differ from those of whole plants reproducing either strictly sexually, or with a combination of sexual and clonal mechanisms. Contrary to the initial expectation from the mutation accumulation theory of senescence, ramets of clonal plants were more likely to exhibit senescence than those species employing sexual reproduction. I discuss why these comparisons between ramets and genets are useful, as well as its implications and future directions for ageing research.     

Ecological and Evolutionary Implications of Bird Pollination

This paper addresses the question of how, and under what ecologicalcircumstances, bird pollination will be optimal for a plant,and which or how many of the available nectar-feeding bird specieswill be optimal pollen vectors. Pollination by birds is energetically expensive for the plants,and should accur only when birds can mediate optimal patternsof pollen flow and seed set. Each nectar-feeding bird has potentialadvantages and disadvantages as a pollen vector, related toits size, morphology, and foraging behavior. Which availablebird is the optimal pollinator depends on the plant's growthhabit, spatial distribution, and breeding system. The variousadaptations shown by plants favoring one pollinator over anotherall revolve around the secretion of nectar and the manner ofpresenting it to the birds. However, other aspects of plantmorphology, physiology, ecology, or life cycle may affect theproduction and presentation of nectar, and influence plant-pollinatorcoevolution. Many question remain regarding the interrelationsbetween pollination and the total biology of the plant; birdpollination systems may prove fruitful in yielding meaningfulanswers.     

Computer-assisted phenotype characterization for genetic research in psychiatry

Psychiatric disorders differ from other complex phenotypes in their lack of objectively assessable biological markers that contribute to the establishment of a research diagnosis for genetic studies. To nevertheless allow for the delineation of genetically meaningful diagnostic entities for psychiatric genetic research, comprehensive phenotype characterization procedures are required. It is widely agreed that these should include the standardized assessment of life-time clinical symptomatology, sociodemographic, and environmental factors. Data should be based on several sources, i.e. diagnostic interviews with probands and their relatives as well as a thorough review of medical records, and final assignment of diagnosis should follow robust algorithms (i.e. best-estimate procedures, consensus diagnosis). Here, we outline a practical implementation of such a phenotype characterization strategy, including patient recruitment, study enrolment procedures, comprehensive diagnostic assessment, and data management. We argue that successful psychiatric phenotype characterization requires flexible tools. For this purpose, we have developed a computer-assisted phenotype characterization inventory, built around the backbone of a relational database. It allows for the straightforward assessment of symptoms, automated error checks and diagnostic assignment, easily manageable data storage and handling, and flexible data transfer between various research centers even across language barriers, while at the same time keeping up with the highest standards for the protection of sensitive patient data.     

Screening for understanding of research in the inpatient psychiatry setting

People with mental illness constitute a substantial proportion of smokers and an important population for smoking cessation research. Obtaining informed consent in this population is a critical ethical endeavor. We examined performance on a three-item instrument (3Q) designed to screen for understanding of several key elements of research: study purpose, risks, and benefits. Patients were clinically diagnosed with primary unipolar depression (n = 40), a primary psychotic disorder (n = 32), both mood and psychotic disorders (n = 17), and primary bipolar disorder (n = 14). Among an ethnically diverse sample of 124 psychiatric inpatients approached for a smoking cessation trial, 107 (86%) performed adequately on the 3Q (i.e., obtained a score of at least 3 out of a possible 6). Patients were better able to identify the study risks and benefits than to describe the study purpose. The 3Q appears to be a useful tool for researchers working with vulnerable psychiatric patients.     

Evolutionary Analysis of Phycobiliproteins: Implications for Their Structural and Functional Relationships

Phycobiliproteins, together with linker polypeptides and various chromophores, are basic building blocks of phycobilisomes, a supramolecular complex with a light-harvesting function in cyanobacteria and red algae. Previous studies suggest that the different types of phycobiliproteins and the linker polypeptides originated from the same ancestor. Here we retrieve the phycobilisome-related genes from the well-annotated and even unfinished cyanobacteria genomes and find that many sites with elevated d _N /d _S ratios in different phycobiliprotein lineages are located in the chromophore-binding domain and the helical hairpin domains (X and Y). Covariation analyses also reveal that these sites are significantly correlated, showing strong evidence of the functional-structural importance of interactions among these residues. The potential selective pressure driving the diversification of phycobiliproteins may be related to the phycobiliprotein-chromophore microenvironment formation and the subunits interaction. Sites and genes identified here would provide targets for further research on the structural-functional role of these residues and energy transfer through the chromophores. [Reviewing Editor: Dr. Rasmus Nielsen]     

Questioning current definitions for breastfeeding research

ABSTRACT: BACKGROUND: The aim of this paper is to examine how breastfeeding is defined for research purposes. DISCUSSION: Current breastfeeding definitions focus on the amount of breast milk an infant receives and do not encompass how a baby is fed. Our concerns are that key variables are not measured when mothers are pumping or expressing their milk and bottle feeding. It seems the breastfeeding relationship is not considered in the definition. CONCLUSION: While we appreciate the implications of full versus partial breastfeeding in research studies, we also believe the method of infant feeding to be significant. Researchers should develop new definitions.     

Systematic and Evolutionary Implications of Parthenogenesis in the Hymenoptera

SYNOPSIS. Two types of parthenogenesis, arrhenotoky and thelytoky,exist in the Hymenoptera. Arrhenotoky, the development of malesfrom unfertilized eggs, is present in all wasps and bees. Thelytoky,the development of diploid females from unfertilized eggs, ispresent in a few species. Two types of thelytoky, apomixis andautomixis, are known. Most thelytokous Hymenoptera are automictic.No meiosis, only mitosis, occurs in apomixis. Meiosis does occurin automixis, allowing crossing-over and segregation of genes.Advantages of thelytoky are that heterotic combinations becomefixed, gene loss is reduced, and reproduction requires onlya single individual. One advantage of arrhenotoky is that geneticload in males is eliminated. Both environmental and geneticfactors contribute to sex-determination in the haplodiploidsystem of Hymenoptera. Haplodiploidy can facilitate the evolutionof social behavior. Parthenogenesis creates some taxonomic problemssince thelytokous clones do not fit the generally accepted biologicalspecies concept. Some members of bisexual populations probablyacquirethelytoky, forming their own clones, races, or species.     

Comparisons of Two Large Phaeoviral Genomes and Evolutionary Implications

The evolution of viral genomes has recently attracted considerable attention. We compare the sequences of two large viral genomes, EsV-1 and FirrV-1, belonging to the family of phaeoviruses which infect different species of marine brown algae. Although their genomes differ substantially in size, these viruses share similar morphologies and similar latent infection cycles. In fact, sequence comparisons show that the viruses have more than 60% of their genes in common. However, the order of genes is completely different in the two genomes, suggesting that extensive recombinational events in addition to several large deletions had occurred during the separate evolutionary routes from a common ancestor. We investigated genes encoding components of signal transduction pathways and genes encoding replicative functions in more detail. We found that the two genomes possess different, although overlapping, sets of genes in both classes, suggesting that different genes from each class were lost, perhaps randomly, after the separate evolution from an ancestral genome. Random loss would also account for the fact that more than one-third of the genes in one viral genome has no counterparts in the other genome. We speculate that the ancestral genome belonged to a cellular organism that had once invaded a primordial brown algal host.     

Evolutionary Implications of Changing Nutritional Patterns in Human Populations

Malnutrition is a widespread problem in the tropical regions of the world, the same areas which are believed to be man's ancestral home. Much of the adaptive complex characterizing contemporary Homo sapiens was assembled during the period of at least partial reliance on dietary intake of animal protein. Adjustments to low protein intake are most difficult during the period of growth and development. Selection against individuals unable to make suitable adjustments exerts pressure on the human population to retain adaptability while maintaining appropriate body proportions and sexual dimorphisms for body size .     

Some fallacies in the computation of paternity probabilities.

Legal identification of fathers by means of a "paternity probability" has been used in European courts for decades, and has recently been introduced into American courts and accepted by some of them. The voluminous literature on this topic contains virtually no fundamental criticism of the logical basis for the probabilistic computations. Here I suggest that the "paternity probability" suffers from three basic fallacies: (1) contrary to claims, the figure is not, in fact, the probability that the alleged father is the true father, (2) the denominator of the likelihood ratio used in the computation is driven by (sometimes self-contradictory) assumptions and is not based on facts, and (3) post-inclusionary computations are based on speculation about genotypes that does not constitute scientific evidence. It is recommended that pending the resolution of these difficulties "paternity probabilities" should not be computed or introduced as positive evidence of paternity.     

Unraveling the Entry Mechanism of Baculoviruses and Its Evolutionary Implications

The entry of baculovirus budded virus into host cells is mediated by two distinct types of envelope fusion proteins (EFPs), GP64 and F protein. Phylogenetic analysis suggested that F proteins were ancestral baculovirus EFPs, whereas GP64 was acquired by progenitor group I alphabaculovirus more recently and may have stimulated the formation of the group I lineage. This study was designed to experimentally recapitulate a possible major step in the evolution of baculoviruses. We demonstrated that the infectivity of an F-null group II alphabaculovirus (Helicoverpa armigera nucleopolyhedrovirus [HearNPV]) can be functionally rescued by coinsertion of GP64 along with the nonfusogenic F^def (furin site mutated HaF) from HearNPV. Interestingly, HearNPV enters cells by endocytosis and, less efficiently, by direct membrane fusion at low pH. However, this recombinant HearNPV coexpressing F^def and GP64 mimicked group I virus not only in its EFP composition but also in its abilities to enter host cells via low-pH-triggered direct fusion pathway. Neutralization assays indicated that the nonfusogenic F proteins contribute mainly to binding to susceptible cells, while GP64 contributes to fusion. Coinsertion of GP64 with an F-like protein (Ac23) from group I virus led to efficient rescue of an F-null group II virus. In summary, these recombinant viruses and their entry modes are considered to resemble an evolutionary event of the acquisition of GP64 by an ancestral group I virus and subsequent adaptive inactivation of the original F protein. The study described here provides the first experimental evidence to support the hypothesis of the evolution of baculovirus EFPs.     

Evolutionary Implications of Dental Eruption in Dasypus (Xenarthra)

Late eruption of the permanent dentition was recently proposed as a shared anatomical feature of endemic African mammals (Afrotheria), with anecdotal reports indicating that it is also present in dasypodids (armadillos). In order to clarify this question, and address the possiblity that late eruption is shared by afrotherians and dasypodids, we quantified the eruption of permanent teeth in Dasypus, focusing on growth series of D. hybridus and D. novemcinctus. This genus is the only known xenarthran that retains two functional generations of teeth. Its adult dentition typically consists of eight upper and eight lower ever-growing (or euhypsodont) molariforms, with no premaxillary teeth. All but the posterior-most tooth are replaced, consistent with the identification of a single molar locus in each series. Comparison of dental replacement and skull metrics reveals that most specimens reach adult size with none or few erupted permanent teeth. This pattern of growth occurring prior to the full eruption of the dentition is similar to that observed in most afrotherians. The condition observed in Dasypus and many afrotherians differs from that of most other mammals, in which the permanent dentition erupts during (not after) growth, and is complete at or near the attainment of sexual maturity and adult body size. The suture closure sequence of basicranial and postcranial epiphyses does not correlate well with dental eruption. The basal phylogenetic position of the taxon within dasypodids suggests that diphyodonty and late dental replacement represent the condition of early xenarthrans. Additionally, the inferred reduction in the number of molars to a single locus and the multiplication of premolars represent rare features for any living mammal, but may represent apomorphic characters for Dasypus.     

Pelage Color Variation of Macaca arctoides and Its Evolutionary Implications

Stump-tailed macaques (Macaca arctoides) exhibit significant intraspecific variation in pelage color. Based on their pelage color and geographical distribution, they are classified into 2 subspecies: northern bright brown Macaca arctoides arctoides and southern black Macaca arctoides melanota. However, studies on the natural population are extremely scarce, and researchers have occasionally questioned the subspecific classification. We quantitatively examined pelage color variation of Macaca arctoides in 3 free-ranging populations in Thailand. Pelage color difference between populations is significant. The population distributed south of the Isthmus of Kra showed wide intrapopulational variation, including bright brown, dark brown, and completely black, whereas the northern populations primarily had dark brown hairs. Thus, we conclude that one cannot classify the color variants into subspecies. Further, we hypothesize that the distinctive polymorphism in southern Thailand resulted from geographical isolation caused by the Pleistocene eustatic fluctuations and subsequent recovery of land connection and subsequent gene flow.     

Unique Dental Morphology of Homo floresiensis and Its Evolutionary Implications

Homo floresiensis is an extinct, diminutive hominin species discovered in the Late Pleistocene deposits of Liang Bua cave, Flores, eastern Indonesia. The nature and evolutionary origins of H. floresiensis’ unique physical characters have been intensively debated. Based on extensive comparisons using linear metric analyses, crown contour analyses, and other trait-by-trait morphological comparisons, we report here that the dental remains from multiple individuals indicate that H. floresiensis had primitive canine-premolar and advanced molar morphologies, a combination of dental traits unknown in any other hominin species. The primitive aspects are comparable to H. erectus from the Early Pleistocene, whereas some of the molar morphologies are more progressive even compared to those of modern humans. This evidence contradicts the earlier claim of an entirely modern human-like dental morphology of H. floresiensis, while at the same time does not support the hypothesis that H. floresiensis originated from a much older H. habilis or Australopithecus-like small-brained hominin species currently unknown in the Asian fossil record. These results are however consistent with the alternative hypothesis that H. floresiensis derived from an earlier Asian Homo erectus population and experienced substantial body and brain size dwarfism in an isolated insular setting. The dentition of H. floresiensis is not a simple, scaled-down version of earlier hominins.