Individual mRNA expression profiles reveal the effects of specific microRNAs

BACKGROUND: MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level. We sought, therefore, to determine whether a general lowering of predicted target gene mRNA expression by endogenous miRNAs was detectable within microarray gene expression profiles. RESULTS: The target gene sets predicted for each miRNA were mapped onto known gene expression data from a range of tissues. Whether considering mean absolute target gene expression, rank sum tests or 'ranked ratios', many miRNAs with significantly reduced target gene expression corresponded to those known to be expressed in the cognate tissue. Expression levels of miRNAs with reduced target mRNA levels were higher than those of miRNAs with no detectable effect on mRNA expression. Analysis of microarray data gathered after artificial perturbation of expression of a specific miRNA confirmed the predicted increase or decrease in influence of the altered miRNA upon mRNA levels. Strongest associations were observed with targets predicted by TargetScan. CONCLUSION: We have demonstrated that the effect of a miRNA on its target mRNAs' levels can be measured within a single gene expression profile. This emphasizes the extent of this mode of regulation in vivo and confirms that many of the predicted miRNA-mRNA interactions are correct. The success of this approach has revealed the vast potential for extracting information about miRNA function from gene expression profiles.

Phylogeographic insights into cryptic glacial refugia

The glacial episodes of the Quaternary (2.6 million years ago–present) were a major factor in shaping the present-day distributions of extant flora and fauna, with expansions and contractions of the ice sheets rendering large areas uninhabitable for most species. Fossil records suggest that many species survived glacial maxima by retreating to refugia, usually at lower latitudes. Recently, phylogeographic studies have given support to the existence of previously unknown, or cryptic, refugia. Here we summarise many of these insights into the glacial histories of species in cryptic refugia gained through phylogeographic approaches. Understanding such refugia might be important as the Earth heads into another period of climate change, in terms of predicting the effects on species distribution and survival.

Monoamines and decision making during contests in the hermit crab Pagurus bernhardus

During fights animals are expected to make a series of strategic decisions that involve interactions between information about the contest and the individual's nervous system that produce a change in behaviour. Biogenic monoamines such as serotonin ('5-HT') and dopamine are thought to prime decision-making centres for appropriate responses during aggressive interactions in crustaceans, and circulating levels vary both between individuals and during agonistic encounters. Aminergenic systems operate in diverse animal taxa and in this study we assayed circulating levels of S-HT and dopamine following shell fights in the common European hermit crab, Pagurus bernhardus. The two roles in these fights, attacker and defender, perform different activities but, in both, S-HT increased and dopamine declined in response to engaging in a fight. In defenders but not attackers, giving up was correlated with low 5-HT and dopamine. In attackers, motivation to initiate a fight was positively correlated with dopamine levels. Circulating monoamines are therefore involved in decision making during these aggressive encounters. (c) 2007 The Association for the Study of Animal Behaviour Published by Elsevier Ltd. All rights reserved.

Honest and dishonest displays, motivational state and subsequent decisions in hermit crab shell fights

Animal fights are typically preceded by displays and there is debate whether these are always honest. We investigated the prefight period in hermit crabs, Pagurus bernhardus, during which up to four types of display plus other activities that might provide information are performed. We determined how each display influences or predicts various fight decisions, and related these displays to the motivational state of the attacker, as determined by a startle response, and of the motivational state of the defender, as determined by the duration for which it resisted eviction from its shell. Two displays appeared to have consistent but different effects. Cheliped presentation, where the claws were held in a stationary position, often by both crabs but for longer by the larger, seemed to be honest, and allowed for mutual size assessment. This display enhanced the motivation and the success of the larger crab. In contrast, cheliped extension, involving the rapid thrust of the open chelae towards the opponent, did not seem to allow for mutual size assessment and may contain an element of bluff. It was performed more by the smaller crab and enhanced its success. The complexity of displays in this species appears to allow for both honesty and manipulation.

Self-assessment by males during energetically costly contests over precopula females in amphipods

In animal contests, individuals can either engage in mutual assessment of both their own and their opponent's resource-holding potential (RHP) and adjust their behaviour according to estimated differences, or instead persist in accordance with thresholds determined by assessment of just their own RHP. We examined the predictions of alternative mutual assessment and self-assessment models for decision rules in contest resolution during struggles between males over females in precopula in the amphipod Gammarus pulex. Contest duration was positively related to the weight of the loser but not the weight of the winner. Our results support the hypothesis that males rely on information about their own RHP in determining contest behaviour and do not use information about their opponent. Fighting was energetically costly, and energy reserves were depleted during contests. Contest duration was associated with the physiological state of the loser (but not the winner) at the end of the contest, and to a lesser extent his size, further supporting self-assessment. (c) 2006 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Sexual cannibalism and mate choice

Sexual cannibalism, where a female kills and consumes a courting male, represents an extreme form of sexual conflict and has been proposed as a mechanism of mate choice. We evaluate the evidence for mate choice through premating sexual cannibalism via mate rejection, other indirect mechanisms of mate 'choice' and choice in postmating sexual cannibalism. We highlight a paucity of investigations, particularly of field studies, and note gaps in our knowledge. There is empirical support for the size-dependent sexual cannibalism predicted by mate choice through premating sexual cannibalism. This may represent mate choice operating on absolute male size but it could be a by-product of female foraging behaviour and greater vulnerability of relatively smaller males. Thus, indirect mate choice is as plausible an explanation of size-dependent sexual cannibalism as is direct mate choice based on discrimination of male traits. Direct female choice, mediated through premating sexual cannibalism, has yet to be demonstrated. We suggest a framework for distinguishing direct and indirect choice and note an absence of information on which to test it. There is evidence for sequential mate choice in postmating sexual cannibalism, but the nature or basis of the female's discriminatory behaviour remains unclear. Costs and long-term fitness benefits of the putative mate choice have been largely ignored. Reversed sexual cannibalism, in which the male eats the female, presumably occurs when the gain from food is high and potential gain from mating low and probably has little to do with mate choice. (c) 2005 The Association for the Study of Animal Behaviour Published by Elsevier Ltd. All rights reserved.

Rapid change in energy status in fighting animals: causes and effects of strategic decisions

Energetic costs of fighting, such as high lactate or low glucose, have been shown in a range of species to correlate with the decisions made by each opponent, particularly the decision by one opponent, the 'loser', to end the fight by 'giving up'. Studies based on complete fights of differing duration, however, do not provide information on the changes in the physiological correlates of fighting that may take place during the course of the encounter, or how these changes may influence the capability and decisions of the contestants. We interrupted fights between hermit crabs, Pagurus bernhardus, at specific points, and related energy status to the preceding activities. Costs rose quickly with a rapid accumulation of lactic acid in attackers and declining muscular glycogen in defenders. Changes in physiological status appeared much earlier than the changes in behaviour that they may have caused. Furthermore, some physiological changes might have been an effect, rather than the cause, of fight decisions. (c) 2005 The Association for the Study of Animal Behaviour Published by Elsevier Ltd. All rights reserved.

Size-assortative pairing in Gammarus pulex (Crustacea : Amphipoda): a test of the timing hypothesis

We present the first empirical test of the timing hypothesis regarding the generation of size-assortative pairing in amphipods. The timing hypothesis proposes that, since large males are better able to afford the costs of mate guarding than small males, the former can take larger females into precopula earlier in the female moult cycle than is feasible for the latter. This leaves small males to form pairs with smaller females closer to moult, thus generating size assortment. We presented male Gammarus pulex, collected both in precopula and as singletons, with females that were (1) previously guarded and therefore near to copulatory moult and (2) previously unguarded and therefore far from copulatory moult. This comparison tested the prediction of the timing hypothesis, that size assortment should break down when the opportunity for time-based male decisions is removed, but that size assortment should occur where timing is not disrupted. Counter to the hypothesis, we found that size assortment did not break down upon removal of the time factor. Large males tended to initiate mate guarding earlier than small males in both female moult groups. However, only in the previously unguarded group did large males guard for longer than small males. This result suggests that, although size assortment occurred in all groups, the causative mechanisms that generated this pattern may differ between these groups. We therefore consider the possible importance of mechanisms such as aggression, simultaneous manipulation of females and female resistance in producing size assortment where males encounter numerous females that are close to moult. We also observed that prior recent guarding experience by males had no effect on latency to guard or size-assortative pairing. (C) 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.

Maternal care in the rockpool amphipod Apherusa jurinei: developmental and environmental cues

There is evidence that active, pre-emergence maternal brood care in amphipod crustaceans may be associated with 'harsh' environmental conditions. We examined, in the rockpool amphipod Apherusa jurinei, behavioural activities that may function as a form of active brood care. Only ovigerous females showed 'curl' and 'stretch' activities, with consequent flushing of the brood pouch and cycling of the eggs therein. There was a significant decline in these activities as embryonic development advanced and brood care almost ceased when well-developed embryos showed a heart pulse and self-ventilation. We propose that this pattern of brood care reflects changes in the physiological requirements of embryos as they develop within the egg membrane. In addition, ovigerous females showed significantly higher levels of brood care under lowered oxygen conditions. They achieved this by increasing the average duration of the 'stretch' component, with other brood care components remaining constant. Thus, developmental and environmental cues alter the components of active brood care in distinct ways. Experimental removal showed that the physical presence of eggs in the brood pouch is important in controlling the expression of brood care activities. However, females with all of their eggs removed continued to brood at low levels, suggesting that a maternal state also controls brood care. The sophisticated expression of active maternal brood care in amphipods under 'harsh' environmental conditions such as rockpools has implications both for individual reproductive success and the distribution and abundance of brooding versus nonbrooding species. (C) 2002 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour.

Motivational change during shell fights in the hermit crab Pagurus bernhardus

During agonistic interactions the motivation of each contestant is expected to vary because of increased information and changes in fighting ability. In shell fights between hermit crabs over gastropod shells, attackers rap their shell in a series of bouts against that of the defender whereas defenders remain withdrawn into their shells until the encounter is resolved; either the defender is evicted from its shell or the attacker 'gives up' and the defender retains its shell. We assessed the motivational state of attackers for performing rapping by measuring the duration of startle responses elicited by a novel stimulus. We staged fights between pairs of crabs in six different groups defined by the potential gain in shell quality available to attackers (high or low) and by the point at which the novel stimulus was applied (prior to rapping, after one bout or after four bouts). Startle response duration decreased during the first four bouts of fighting and showed a U-shaped relationship with the relative difference in size between the crabs. There was, no difference in startle response duration between high- and low-gain groups. Individuals showing short startle responses were likely to be victorious and we conclude that the relationship between the relative size difference of the opponents and. startle duration reflects that between size difference and the cost of gaining an eviction. (C) 2001 The Association for the Study of Animal Behaviour.

Co-existence of a pair of pelagic planktivorous coregonid fishes

Hypothesis: Ecological specialization facilitates co-existence of Coregonus spp. in Lake Stechlin. A difference in trophic ecology is the dominant means by which the species are ecologically segregated.

Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galapagos sea lion populations

Background: Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki) are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation.
Results: We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis) that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation.
Conclusion: Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations.

Experimental assessment of oyster transfers as a vector for macroalgal introductions

Introduction of non-indigenous species can alter marine communities and ecosystems. In shellfish farming, transfer of livestock, especially oysters, is a common practice and potentially constitutes a pathway for non-indigenous introductions. Many species of seaweeds are believed to have been accidentally introduced in association with these transfers, but there is little direct evidence.

Widespread dispersal of the microsporidian Nosema ceranae, an emergent pathogen of the western honey bee, Apis mellifera

The economically most important honey bee species, Apis mellifera, was formerly considered to be parasitized by one microsporidian, Nosema apis. Recently, [Higes, M., Martin, R., Meana, A., 2006. Nosema ceranae, a new microsporidian parasite in honeybees in Europe, J. Invertebr. Pathol. 92, 93-95] and [Huang, W.-F., Jiang, J.-H., Chen, Y.-W., Wang, C.-H., 2007. A Nosema ceranae isolate from the honeybee Apis mellifera. Apidologie 38, 30-37] used 16S (SSU) rRNA gene sequences to demonstrate the presence of Nosema ceranae in A. mellifera from Spain and Taiwan, respectively. We developed a rapid method to differentiate between N. apis and N. ceranae based on PCR-RFLPs of partial SSU rRNA. The reliability of the method was confirmed by sequencing 29 isolates from across the world (N = 9 isolates gave N. apis RFLPs and sequences, N = 20 isolates gave N. ceranae RFLPs and sequences; 100%, correct classification). We then employed the method to analyze N = 115 isolates from across the world. Our data, combined with N = 36 additional published sequences demonstrate that (i) N. ceranae most likely jumped host to A. mellifera, probably within the last decade, (ii) that host colonies and individuals may be co-infected by both microsporidia species, and that (iii) N. ceranae is now a parasite of A. mellifera across most of the world. The rapid, long-distance dispersal of N. ceranae is likely due to transport of infected honey bees by commercial or hobbyist beekeepers. We discuss the implications of this emergent pathogen for worldwide beekeeping. (c) 2007 Elsevier Inc. All rights reserved.

Rarity and decline in bumblebees - A test of causes and correlates in the Irish fauna

Bees are believed to be in decline across many of the world's ecosystems. Recent studies on British bumblebees proposed alternative theories to explain declines. One study suggested that greater dietary specialization among the rarer bumblebee species makes them more susceptible to decline. A second study disputed this theory and found that declines in British bumblebees were correlated with the size of species' European ranges, leading to the suggestion that climate and habitat specialization may be better indicators of the risk of decline. Here we use a new and independent dataset based on Irish bumblebees to test the generality of these theories. We found that most of the same bumblebee species are declining across the British Isles, but that, within Ireland, a simple food-plant specialization model is inadequate to explain these declines. Furthermore, we found no evidence of a relationship between declines in Irish bumblebees and the size of species' European ranges. However, we demonstrate that the late emerging species have declined in Ireland (and in Britain), and that these species show a statistically significant westward shift to the extremity of their range, probably as a result of changing land use. Irish data support the finding that rare and declining bumblebees are later nesting species, associated with open grassy habitats. We suggest that the widespread replacement of hay with silage in the agricultural landscape, which results in earlier and more frequent mowing and a reduction in late summer wildflowers, has played a major role in bumblebee declines. (C) 2006 Elsevier Ltd. All rights reserved.