Lack of evidence for the match-mismatch hypothesis across terrestrial trophic interactions

Climate change has led to widespread shifts in the timing of key life history events between interacting species (phenological asynchrony) with hypothesized cascading negative fitness impacts on one or more of the interacting species—often termed ‘mismatch’. Yet, predicting the types of systems prone to mismatch remains a major hurdle. Recent reviews have argued that many studies do not provide strong evidence of the underlying match-mismatch hypothesis, but none have quantitatively analysed support for it. Here, we test the hypothesis by estimating the prevalence of mismatch across antagonistic trophic interactions in terrestrial systems and then examine whether studies that meet the assumptions of the hypothesis are more likely to find a mismatch. Despite a large range of synchrony to asynchrony, we did not find general support for the hypothesis. Our results thus question the general applicability of this hypothesis in terrestrial systems, but they also suggest specific types of data missing to robustly refute it. We highlight the critical need to define resource seasonality and the window of ‘match’ for the most rigorous tests of the hypothesis. Such efforts are necessary if we want to predict systems where mismatches are likely to occur.     

A Phylogenetic Comparative Study of Bantu Kinship Terminology Finds Limited Support for Its Co-Evolution with Social Organisation

The classification of kin into structured groups is a diverse phenomenon which is ubiquitous in human culture. For populations which are organized into large agropastoral groupings of sedentary residence but not governed within the context of a centralised state, such as our study sample of 83 historical Bantu-speaking groups of sub-Saharan Africa, cultural kinship norms guide all aspects of everyday life and social organization. Such rules operate in part through the use of differing terminological referential systems of familial organization. Although the cross-cultural study of kinship terminology was foundational in Anthropology, few modern studies have made use of statistical advances to further our sparse understanding of the structuring and diversification of terminological systems of kinship over time. In this study we use Bayesian Markov Chain Monte Carlo methods of phylogenetic comparison to investigate the evolution of Bantu kinship terminology and reconstruct the ancestral state and diversification of cousin terminology in this family of sub-Saharan ethnolinguistic groups. Using a phylogenetic tree of Bantu languages, we then test the prominent hypothesis that structured variation in systems of cousin terminology has co-evolved alongside adaptive change in patterns of descent organization, as well as rules of residence. We find limited support for this hypothesis, and argue that the shaping of systems of kinship terminology is a multifactorial process, concluding with possible avenues of future research.     

Nestling coloration is adjusted to parent visual performance in altricial birds irrespective of assumptions on vision system for Laniidae and owls,a reply to Renoult et al.

We have recently published support to the hypothesis that visual systems of parents could affect nestling detectability and, consequently, influences the evolution of nestling colour designs in altricial birds. We provided comparative evidence of an adjustment of nestling colour designs to the visual system of parents that we have found in a comparative study on 22 altricial bird species. In this issue, however, Renoult et al. ( J. Evol. Biol., 2009 ) question some of the assumptions and statistical approaches in our study. Their argumentation relied on two major points: (1) an incorrect assignment of vision system to four out of 22 sampled species in our study; and (2) the use of an incorrect approach for phylogenetic correction of the predicted associations. Here, we discuss in detail re‐assignation of vision systems in that study and propose alternative interpretation for current knowledge on spectrophotometric data of avian pigments. We reanalysed the data by using phylogenetic generalized least squares analyses that account for the alluded limitations of phylogenetically independent contrasts and, in accordance with the hypothesis, confirmed a significant influence of parental visual system on gape coloration. Our results proved to be robust to the assumptions on visual system evolution for Laniidae and nocturnal owls that Renoult et al. ( J. Evol. Biol., 2009 ) study suggested may have flawed our early findings. Thus, the hypothesis that selection has resulted in increased detectability of nestling by adjusting gape coloration to parental visual systems is currently supported by our comparative data.     

OrthoDisease: tracking disease gene orthologs across 100 species

Orthology is one of the most important tools available to modern biology, as it allows making inferences from easily studied model systems to much less tractable systems of interest, such as ourselves. This becomes important not least in the study of genetic diseases. We here review work on the orthology of disease-associated genes and also present an updated version of the InParanoid-based disease orthology database and web site OrthoDisease, with 14-fold increased species coverage since the previous version. Using this resource, we survey the taxonomic distribution of orthologs of human genes involved in different disease categories. The hypothesis that paralogs can mask the effect of deleterious mutations predicts that known heritable disease genes should have fewer close paralogs. We found large-scale support for this hypothesis as significantly fewer duplications were observed for disease genes in the OrthoDisease ortholog groups.     

The scale-precision trade-off in spacial resource foraging by plants: restoring perspective

BACKGROUND AND AIMS: From the results of a comparative study using quantitative standardized assays of the scale and precision of responses of root and shoot systems to resource patchiness, Campbell et al. (1991; Oecologia 87: 532-538) proposed a mechanism of species coexistence in herbaceous communities involving a dynamic equilibrium between, respectively, the coarse- and fine-scale foraging of dominant and subordinate species. The purpose of this paper is to reject a recent assertion that with respect to root systems the scale-precision hypothesis has been falsified. DISCUSSION AND CONCLUSION: Reference to the original papers confirms that the scope of the hypothesis was confined to circumstances (eg. mown meadows) where the vigour of potential dominants is restricted by intermittent removal of biomass. This qualification in the original hypothesis is a crucial omission from the meta-analysis conducted by Kembel and Cahill (2005; American Naturalist 166: 216-230). The original papers also contain examples that illustrate the operation of forms of selection that prevent the development of precise foraging below ground; these also appear to have escaped the attention of recent participants in this field of research.     

The role of endosymbionts in the evolution of haploid-male genetic systems in scale insects (Coccoidea)

There is an extraordinary diversity in genetic systems across species, but this variation remains poorly understood. In part, this is because the mechanisms responsible for transitions between systems are often unknown. A recent hypothesis has suggested that conflict between hosts and endosymbiotic microorganisms over transmission could drive the transition from diplodiploidy to systems with male haploidy (haplodiploidy, including arrhenotoky and paternal genome elimination [PGE]). Here, we present the first formal test of this idea with a comparative analysis across scale insects (Hemiptera: Coccoidea). Scale insects are renowned for their large variation in genetic systems, and multiple transitions between diplodiploidy and haplodiploidy have taken place within this group. Additionally, most species rely on endosymbiotic microorganisms to provide them with essential nutrients lacking in their diet. We show that species harboring endosymbionts are indeed more likely to have a genetic system with male haploidy, which supports the hypothesis that endosymbionts might have played a role in the transition to haplodiploidy. We also extend our analysis to consider the relationship between endosymbiont presence and transitions to parthenogenesis. Although in scale insects there is no such overall association, species harboring eukaryote endosymbionts were more likely to be parthenogenetic than those with bacterial symbionts. These results support the idea that intergenomic conflict can drive the evolution of novel genetic systems and affect host reproduction.     

Landscape variables affecting fishery yield in lake systems of the Central Amazon region, Brazil

According to fisheries data, lakes are important systems for fish production in the Amazon basin. However, there is no information about the relationship between landscape variables and fishing yield that allows foresight into potential resource exploitation in this environment. The present study aims to evaluate this relationship with the hypothesis: lakes of different shapes give the same fishery yield in the Amazon, after considering the effects of lake size, distance to the river, fishing effort, fuel and ice used. Fishery data from 1994 to 1996 were analyzed with regard to 3228 trips on 50 lakes of the main white water tributaries of the Amazon basin. Analysis of covariance was applied to test this hypothesis. With variables such as fishing grounds access, fishing effort and lake shape the model explained a significant 72% of variabilities in the fisheries yield. Fishing yields among lake systems were different, thus the null hypothesis was rejected (P < 0.05). Results indicate that dendritic lakes far distant from the main river have greater productivity than floodplain lakes because there are more habitats of fish refuge for reproduction and feed available to the fish; there are also more limitations to access by predators.     

Empirical perspectives on species borders: from traditional biogeography to global change

In this paper we will outline several empirical approaches to developing and testing hypotheses about the determinants of species borders. We highlight environmental change as an important opportunity – arguing that these unplanned, large-scale manipulations can be used to study mechanisms which limit species distributions. Our discussion will emphasize three main ideas. First, we review the traditional biogeographic approach. We show how modern analytical and computer techniques have improved this approach and generated important new hypotheses concerning species' range determinants. However, abilities to test those hypotheses continue to be limited. Next we look at how the additions of temporal data, field and lab experimentation, biological details and replication, when applied to systems that have been the subject of classical biogeographic studies, have been used to support or refute hypotheses on range determinants. Such a multi-faceted approach adds rigor, consistency and plausible mechanisms to the study of species ranges, and has been especially fruitful in the study of climate and species' ranges. Lastly, we present an alternative avenue for exploration of range-limiting mechanisms which has been under-utilized. We argue that carefully designed comparisons and contrasts between groups of species or systems provide a powerful tool for examining hypotheses on species' borders. The seasonality hypothesis as an explanation for Rapoport's rule serves as a model of this approach. A test is constructed by comparing patterns of seasonality and range size among marine and terrestrial systems. The seasonality hypothesis is not supported.     

时距估计长度效应的研究述评

时距估计的长度效应,是指不同长度的时距存在不同的加工机制。从行为反应、神经心理以及脑成像三个领域对有关长度效应的研究进行综述。行为实验多用双任务范式,考察涉及工作记忆的非时间任务对长短时距加工的影响,行为实验的结果不一致,采用双任务范式的实验证据一般不能证明长度效应的存在。而有关脑机制的神经心理与脑成像研究结果一致,支持存在长度效应,但对于两个计时机制各自涉及的脑区以及脑电活动模式仍没有定论。长短时距可能因为所用任务特征不同采用不同计时机制,今后的研究将重点探讨特定任务是否涉及不同的计时机制。     

Revisiting the particular role of host shifts in initiating insect speciation

The notion that shifts to new hosts can initiate insect speciation is more than 150 years old, yet widespread conflation with paradigms of sympatric speciation has led to confusion about how much support exists for this hypothesis. Here, we review 85 insect systems and evaluate the relationship between host shifting, reproductive isolation, and speciation. We sort insects into five categories: (1) systems in which a host shift has initiated speciation; (2) systems in which a host shift has made a contribution to speciation; (3) systems in which a host shift has caused the evolution of new reproductive isolating barriers; (4) systems with host‐associated genetic differences; and (5) systems with no evidence of host‐associated genetic differences. We find host‐associated genetic structure in 65 systems, 43 of which show that host shifts have resulted in the evolution of new reproductive barriers. Twenty‐six of the latter also support a role for host shifts in speciation, including eight studies that definitively support the hypothesis that a host shift has initiated speciation. While this review is agnostic as to the fraction of all insect speciation events to which host shifts have contributed, it clarifies that host shifts absolutely can and do initiate speciation.     

EVOLUTION OF PLANT POLLINATION SYSTEMS: HYPOTHESES AND TESTS WITH THE NEOTROPICAL VINE DALECHAMPIA

The results of pollination and mating-system studies were integrated with a phylogenetic study of 40 Neotropical species of Dalechampia L. (Euphorbiaceae) to reconstruct the history of evolutionary change in pollination systems. The results of this analysis were treated as a hypothesis and tested for circularity problems and robustness in the face of changes in the data set. The historical hypothesis was used to make specific predictions about details of pollination ecology and reward biochemistry; the predictions were supported by independent observations. I conclude that pollination systems in Dalechampia have been evolutionarily labile, relative to most morphological features, with repeated parallelisms and reversals. Transitions among the three pollination systems evolved by Dalechampia (pollination by resin-collecting bees, fragrance-collecting male euglossine bees, and pollen-collecting bees) have been facilitated by biochemical exaptation (preadaptation). Pollination by male euglossine bees is relatively rare in the genus but has originated independently three to four times. In contrast, pollination by resin-collecting female bees is very common, but has originated only once. Eighty-six to 97% of transitions between pollination systems involved an intermediate phase during which both old and new pollinators were effective, but 3 to 14% of transitions may have been “instantaneous,” lacking the intermediate phase. Clades of species secreting resin rewards are about 10 times as species rich as clades of species secreting fragrance rewards; circumstantial evidence suggests that different extinction rates may be responsible for this difference. Relatively allogamous (cross-pollinating) species have evolved from more autogamous (self-pollinating) species up to 13 times, and autogamous species have evolved from more allogamous ones up to 11 times. Species occurring in disturbed habitats are facultatively autogamous, whereas species of undisturbed habitats are often highly allogamous.     

Foliar stable carbon and nitrogen isotopes in woody Mediterranean species with different life form and post-fire regeneration

Wildfire is an important ecological disturbance factor in most Mediterranean ecosystems. In the Mediterranean Basin, most shrub species can regenerate after fire by resprouting or seeding. Here, we hypothesize that post-fire regenerative syndromes may potentially co-vary with traits directly related to functional properties involved in resource use. Thus, seeders with a shorter life span and smaller size would have lower water-use efficiency (WUE) than re-sprouting species and would take up nutrients such as nitrogen from more superficial parts of the soil. To test this hypothesis, we compared leaf ¹³C and ¹⁵N signatures from 29 co-existing species with different post-fire regeneration strategies. We also considered life form as an additional explanatory variable of the differences between post-fire regenerative groups. Our data support the hypothesis that seeder species (which mostly evolved in the Quaternary under a Mediterranean climate) have lower WUE and less stomatal control than non-seeders (many of which evolved under different climatic conditions in the Tertiary) and consequently greater consumption of water per unit biomass. This would be related to their smaller life forms, which tend to have lower WUE and shorter life and leaf lifespan. Differences in ¹⁵N also support the hypothesis that resprouters have deeper root systems than non-resprouters. The study supports the hypothesis of an overlap between plant functional traits and plant attributes describing post-disturbance resilience.     

On principles of organization of polyreplicon systems

Summary Principles for the acceptability of replicons and polyreplicon systems are formulated, based on the postulated single reproduction of all the components of these systems in each reduplication cycle. On this basis the diverse variants of properties inherent to these systems and their punctuation marks (replicators and terminators) are discussed. The problem of the existence of terminators of reduplication is also considered.Variants of linear polyreplicon systems with identical punctuation are examined. Rules determining the acceptability of different aberrations are put forward. The following variants are unacceptable: inversions the ends of which lie in replicons with the same orientation; non-reciprocal translocations where the ends lie in replicons with opposite orientation; reciprocal translocations of two fragments differing in the orientation of the end replicons; all deletions. It is shown that polyreplicon systems in which all the replicons have the same orientation are subject to maximal losses due to aberrations, whereas systems consisting of two replicon groups equal in total length and having opposite orientation bear minimal losses.The following conclusions are drawn from the comparison of these rules and the analysis of the experimental data: 1)-If terminators exist, replicons of eukaryote chromosomes, in which acceptable aberrations are found, do not overlap and have the same punctuation. 2)- In this case, the alternating orientation of replicons in mammalian chromosomes corresponds to minimal aberrational losses. A hypothesis is proposed for the evolutionary pathway along which linear polyreplicon systems of eukaryotes may have appeared. According to this hypothesis, circular replicons of prokaryotes have united by means of recombination into systems with subsequent selection of variants based on minimal aberrational losses.     

EVOLUTION OF HAPLODIPLOIDY IN DERMANYSSINE MITES (ACARI: MESOSTIGMATA)

Haplodiploidy, a widespread phenomenon in which males are haploid and females are diploid, can be caused by a number of different underlying genetic systems. In the most common of these, arrhenotoky, males arise from unfertilized eggs, whereas females arise from fertilized eggs. In another system, pseudoarrhenotoky, males arise from fertilized eggs, but they eliminate the paternal genome at some point prior to spermatogenesis, with the consequence that they do not pass this genome to their offspring. In 1931 Schrader and Hughes-Schrader suggested that arrhenotoky arises through a series of stages involving pseudoarrhenotokous systems such as those found in many scale insects (Homoptera: Coccoidea), however, their hypothesis has been largely ignored. We have used a phylogenetic analysis of 751 base pairs of 28S rDNA from a group of mites (Mesostigmata: Dermanyssina) that contains arrhenotokous, pseudoarrhenotokous, and ancestrally diplodiploid members to test this hypothesis. Neighbor-joining, maximum-parsimony, and maximum-likelihood methods all indicate that the arrhenotokous members of this group form a clade that arose from a pseudoarrhenotokous ancestor, rather than directly from a diplodiploid one. This provides unequivocal support for the hypothesis of Schrader and Hughes-Schrader. The wider implications of this result for the evolution of uniparental genetic systems are discussed.     

Molecular self-organization and multiple equilibrium systems

We have compared different types of natural self-organizing systems: crystal-like formation of multimolecular systems were conferred with self-organization in active media and dissipative structure formation. The comparison revealed a common feature of all such systems. They all have bi-(multi-)stable states. We propose a hypothesis that self-organization is impossible in systems that could not have bi-(multi-)stable states.     

Evolutionary changes of the importance of olfaction in cetaceans based on the olfactory marker protein gene

Odontocetes and mysticetes are two extant suborders of cetaceans. It is reported that the former have no sense of olfaction, while the latter can smell in air. To explain the ecological reason why mysticetes still retain their sense of smell, two hypotheses have been proposed — the echolocation-priority hypothesis, which assumes that the acquisition of echolocation causes the reduction of the importance of olfaction, and the filter-feeder hypothesis, which assumes that olfactory ability is important for filter-feeders to locate their prey because clouds of plankton give off a peculiar odor. The olfactory marker protein (OMP) is almost exclusively expressed in vertebrate olfactory receptor neurons, and is considered to play important roles in olfactory systems. In this study, full-length open reading frames of OMP genes were identified in 6 cetacean species and we analyzed the nonsynonymous to synonymous substitution rate ratio based on the maximum likelihood method. The evolutionary changes of the selective pressures on OMP genes did fit better to the filter-feeder hypothesis than to the echolocation-priority hypothesis. In addition, no pseudogenization mutations are found in all five odontocetes OMP genes investigated in this study. It may suggest that OMP retains some function even in ‘anosmic’ odontocetes.     

Transmembrane movement of exogenous long-chain fatty acids: proteins, enzymes, and vectorial esterification.

The processes that govern the regulated transport of long-chain fatty acids across the plasma membrane are quite distinct compared to counterparts involved in the transport of hydrophilic solutes such as sugars and amino acids. These differences stem from the unique physical and chemical properties of long-chain fatty acids. To date, several distinct classes of proteins have been shown to participate in the transport of exogenous long-chain fatty acids across the membrane. More recent work is consistent with the hypothesis that in addition to the role played by proteins in this process, there is a diffusional component which must also be considered. Central to the development of this hypothesis are the appropriate experimental systems, which can be manipulated using the tools of molecular genetics. Escherichia coli and Saccharomyces cerevisiae are ideally suited as model systems to study this process in that both (i) exhibit saturable long-chain fatty acid transport at low ligand concentrations, (ii) have specific membrane-bound and membrane-associated proteins that are components of the transport apparatus, and (iii) can be easily manipulated using the tools of molecular genetics. In both systems, central players in the process of fatty acid transport are fatty acid transport proteins (FadL or Fat1p) and fatty acyl coenzyme A (CoA) synthetase (FACS; fatty acid CoA ligase [AMP forming] [EC 6.2.1.3]). FACS appears to function in concert with FadL (bacteria) or Fat1p (yeast) in the conversion of the free fatty acid to CoA thioesters concomitant with transport, thereby rendering this process unidirectional. This process of trapping transported fatty acids represents one fundamental mechanism operational in the transport of exogenous fatty acids.     

Gene expression profiling – Clusters of possibilities

Advances in qPCR technology allow studies of increasingly large systems comprising many genes and samples. The increasing data sizes allow expression profiling both in the gene and the samples dimension while also putting higher demands on sound statistical analysis and expertise to handle and interpret its results. We distinguish between exploratory and confirmatory statistical studies. In this paper we demonstrate several techniques available for exploratory studies on a system of Xenopus laevis development from egg to tadpole. Techniques include hierarchical clustering, heatmap, principal component analysis and self-organizing maps. We stress that even though exploratory studies are excellent for generating hypotheses, results have not been proven statistically significant until an independent confirmatory study has been performed. An exploratory study may certainly be valuable in its own right, and there are often not enough resources to report both an exploratory and a confirmatory study at the same time. However, exploratory and confirmatory studies are intimately connected and we would like to raise that awareness among qPCR practitioners. We suggest that scientific reports should always have a hypothesis focus. Reports are either hypothesis generating, from an exploratory study, or hypothesis validating, from a confirmatory study, or both. In either case, we suggest the generated or validated hypotheses be specifically stated.     

Generalized and complementary pollination system in the Andean cactus Echinopsis schickendantzii

The considerable floral diversity present in the cactus family has often been associated with the specificity of its pollinators. However, many cactus pollination systems are generalized as their flowers are pollinated by a wide spectrum of animals. For example, cactus species with white flowers, nocturnal anthesis and extended floral cycles would present generalized pollination systems in which both nocturnal and diurnal visitors could be effective pollinators. In this article, we tested this hypothesis by studying the pollination biology of Echinopsis schickendantzii, an Andean cactus with sphingophilous flowers. In addition, we evaluated whether the cactus’s pollination system is complementary or redundant regarding the relative contributions of nocturnal and diurnal pollinators. Specifically, we studied the floral cycle, the reproductive system and the pollination effectiveness of floral visitors. The flowers of E. schickendantzii are self-incompatible; they opened at crepuscule and have an extended floral cycle. Moths were frequent visitors at night, whereas bees were frequent visitors during the day; both were effective pollinators of the cactus. Our results indicated that the flowers of this species present phenotypic, functional and ecological generalization, and their fruit set is determined by the contributions of both pollinator functional groups, i.e., they have complementary pollination systems. These results support the hypothesis that cacti in the extra-tropical deserts of South America have generalized pollination systems.     

Dopaminergic mechanisms in the pathogenesis of schizophrenia.

The dopamine hypothesis of schizophrenia has been the dominant theoretical construction guiding research and treatment of the schizophrenic disorders over the past generation. This hypothesis, in its simplest guise, posits the presence of a functional alteration in central dopaminergic systems in the brains of schizophrenic patients. Recent findings have resulted in a greater understanding of the complexity of the central dopaminergic systems and have led to revisions of the hypothesis of a simple functional hyperactivity of central dopaminergic systems. These recent data suggest that there may be regionally restricted changes in the function of the mesotelencephalic dopamine system, and that these changes may be in opposite directions. Such changes may be associated with dysfunctions of interactions between distinct dopaminergic terminal field regions, and may be subserved by functional derangements in other transmitter systems or reflect regionally restricted changes in expression or function of distinct dopamine receptors or catecholamine synthetic enzymes. A recent FASEB symposium reviewed new advances in molecular biology, biochemistry, pharmacology, anatomy, and systems neuroscience as they relate to schizophrenia, and discussed the implications of these data for guiding future research and treatment strategies.