Ideas in Ecology and Evolution最新文献

{"title":"A hypothesis to explain host species differences in resistance to multi-host parasites","authors":"M. Forbes, Julia J. Mlynarek","doi":"10.4033/IEE.2014.7.5.N","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.5.N","url":null,"abstract":"Here, we offer a novel hypothesis to explain why some host species evolve resistance, whereas other related species remain susceptible to a shared parasite species. We first describe instances of single water mite species that are ectoparasitic on different species of host dragonflies, where the mites are killed by resistance mechanisms and have little to no fitness on some host species. This begs the question of why some host species are susceptible, whereas other host species are (nearly) completely resistant. Earlier logic based on parasites exploiting abundant host species at the cost of exploiting rare host species does not explain such instances well. Rather, a hypothesis based on closed populations of some host species being able to evolve parasite recognition is invoked. Parasite recognition is not expected to evolve in host species from more open populations with considerable gene flow across sites, only some sites of which have the parasite species present. The logic of this hypothesis can be explored with simulation models, whereas empirical tests could involve combined approaches using molecular genetics, population genetics, experimental infections and transplantation experiments.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Specificity in parasites with multiple hosts: The view from the hosts' perspective","authors":"G. Lozano","doi":"10.4033/IEE.V7I1.5213","DOIUrl":"https://doi.org/10.4033/IEE.V7I1.5213","url":null,"abstract":"Reminiscent of Dawkins’ analogy using the Necker cube (Dawkins 1983), Forbes and Mlynarek (2014) offer us a different perspective of multi-host parasite systems. Forbes and Mlynarek point out that, traditionally, multi-host parasite systems have been mostly viewed from the perspective of the parasite. Parasites have shorter lifespans and hence, supposedly have the upper hand in the antagonistic coevolutionary race between parasites and host. It is logical to study the problem from the perspective of the party that is more likely to be better adapted. However, Forbes and Mlynarek suggest it is perhaps time to view the problem from the perspective of the hosts, and offer a hypothesis based on the degree of gene flow between host populations affected or unaffected by a given parasite. Forbes and Mlynarek’s ‘coevolutionary release hypothesis’ argues that when some host populations are not exposed to the parasite, gene flow from the unaffected host population hinders the affected host population’s ability to evolve resistance to the parasite. The hypothesis is sound, intuitive, and perhaps long overdue, yet surprisingly, Forbes and Mlynarek are tentative with their predictions, and choose not to fully explore the implications of their idea. They limit their predictions and discussion to the differences in parasite recognition and immunity among host populations. However, the process of parasite resistance is multifaceted and consists of several other layers of protection besides physiological or immunological adaptations. Here, I shall briefly speculate on how the coevolutionary release hypothesis can affect several other related areas, and I shall explore specific predictions and implications of examining multi-host systems from the hosts’ perspective. Behaviour is the first layer of protection against parasitism. Anti-parasitic behaviours are wide-ranging, and include, for example, avoiding infected individuals, simple preening and grooming, avoiding parasite-laden areas or food items, and even self-medication (Hart 1990, Villalba and Provenza 2009, Moore et al. 2013). Many of these behavioural defenses against parasites are learned, and many others are innate. The coevolutionary release hypothesis makes clear predictions about the degree and effectiveness of parasite-avoiding and parasite-defensive behaviours among host populations. The hypothesis predicts that the most effective parasiteprotection behaviours should evolve only in closed populations in which all potential hosts are exposed to the parasite, rather than in open populations. In contrast, the hypothesis makes no predictions about learned defenses—whether or not the host population is open or closed. For at least 30 years now, parasites have featured prominently in the study of sexual selection (Andersson 1994). There is no need here for an extensive review of the main hypotheses, but suffice it to say that, via various mechanisms, parasite resistance is thought to be indicated by ornam","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70236859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lights, camera, science: The utility and growing popularity of film festivals at scientific meetings","authors":"E. Staaterman, Ashwin A. Bhandiwad, Philip M. Gravinese, P. Moeller, Zachary C Reichenbach, A. A. Shantz, D. Shiffman, L. Toth, Alexandria Warneke, A. Gallagher","doi":"10.4033/IEE.2014.7.4.F","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.4.F","url":null,"abstract":"","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70235011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fishing for philosophical phylogenetic foibles","authors":"Root Gorelick","doi":"10.4033/IEE.2014.7.3.C","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.3.C","url":null,"abstract":"","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4033/IEE.2014.7.3.C","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70234971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fishing for significance in phylogenies: too many alternatives for the same outcome, or an appeal to Journal editors","authors":"J. Chiapella, J. Kuhl, P. Demaio, L. Amarilla","doi":"10.4033/IEE.V7I1.5076","DOIUrl":"https://doi.org/10.4033/IEE.V7I1.5076","url":null,"abstract":"The ever increasing number of computer programs developed for phylogenetic research does not necessarily facilitate the construction of biologically relevant phylogenies. Regardless of the algorithm utilized by new software, the vast majority result in treelike graphs. We suggest that a new, more inclusive framework for phylogenetic studies needs to be developed, which includes trees as an alternative in the absence of conflicting signals in the sequence data set. Conflicts are caused by noisy phylogenetic signal deriving from hybridization, allopolyploidy and lateral gene transfer—biological processes that undermine the construction of simple dichotomic bifurcating graphs. A robust framework for determining biologically relevant phylogenetic relationships should include quality analysis of the phylogenetic signal, a thorough determination of homology, analyses for phylogenetic networks, and exploration of the data for character or tree conflicts.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70236846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Self-citation by researchers: narcissism or an inevitable outcome of a cohesive and sustained research program?","authors":"S. Cooke, M. Donaldson","doi":"10.4033/IEE.2014.7.1.E","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.1.E","url":null,"abstract":"Steven J. Cooke (steven_cooke@carleton.ca), Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, Ottawa, Ontario, Canada Michael R. Donaldson (michael.r.donaldson@gmail.com), Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, USA The research community remains focused with enumerating, evaluating, and ranking the research productivity of individual authors despite the apparent shortcomings of doing so. Basic yet widely used citation metrics such as ³WRWDO FLWHV´ (Adam 2002) or ³+LUsch (h) LQGH[´ (Hirsch 2005) require a count of the number of times that a given DXWKRU¶V works are cited. Fortunately there are a variety of electronic bibliometric tools (e.g., Web of Science, Google Scholar, Scopus) that do that work for us. Interestingly, those tools tend to generate default counts that can include self-citations. Self-citations can be defined as occurrences in which the citing and cited papers share at least one author in common (Asknes 2003), although various definitions have been proposed (Fowler and Aksnes 2007, Costas et al. 2010). Self-citations can be easily filtered out with a few clicks to generate ³FRUUHFWHG´ indices (e.g., Schreiber 2007, Brown 2009) or those that discount self-cites (e.g., Ferrara and Romero 2013), but is it necessary to do so? Here, we argue that self-citations need not necessarily be considered a form of narcissistic behavior, and instead could be indicative of a cohesive research program, in which authors refer to their prev-ious relevant works in order to enhance their subsequent contributions to knowledge. When applying for scientific positions, promotions, tenure, or awards, one must decide whether they will report their ³SURGXFWLYLW´ with or without self-citations, or include both. And, those assessing such researchers must decide which they wish to consider and whether they will ³SHQDOL]H´ someone that fails to exclude self-citations. Some individuals may feel that it is abhorrent to include self-citations while others may be indifferent. On the surface, ³VHOI-FLWDWLRQ´ may appear to border on narcissism. However, the argument could also be made that self-citation is in fact an indicator of RQH¶V promin-ence and productivity in their field. Consider a research-er with a focused research program publishing year after year on related topics, with papers building upon ideas and discoveries codified in previous work. One would expect significant reliance on research papers from the same research lab. Indeed, is that not what an ³LGHDO´ research program should look like? Similarly, if one is working in a highly specialized field where there is simply little other research effort, self-citation would be essential. The more productive one is in terms of output in quantity of papers would also inherently lead to greater potential for self-citations. In this sense, it is reasonable to think","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"31 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70234624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Good science depends on good peer review","authors":"M. Hochberg","doi":"10.4033/IEE.2014.7.16.F","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.16.F","url":null,"abstract":"I argue that the quality of both scientific research and how it is communicated is maintained and improved through a process analogous to Darwinian evolution. Maintaining status quo or achieving scientific advances are potentially threatened by ‘costs’, including costs in the effort required to maintain current or attain higher scientific quality, and financial costs of conducting high-level research. I describe through analogy with Darwinian evolution how, without peer-review and editorial oversight, scientific quality is expected to decrease on average in the long run. Several mechanisms are presented which, taken together, can contribute to limiting or counteracting this effect—some of the most promising being reviewer rewards, journal peerage, and education. I conclude that the scientific community needs to be proactive in promoting peer review and the reviewer commons, and ultimately scientific quality, because the erosion effect may be gradual and barely noticeable in the short-term, but have substantial effects over the long-term.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70234637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The journal impact factor contest leads to erosion of quality of peer review","authors":"D. Wardle","doi":"10.4033/IEE.2014.7.17.C","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.17.C","url":null,"abstract":"In his commentary, Hochberg (2014) makes the case that the quality of scientific research is maintained and enhanced over time through a process akin to Darwinian evolution, and that high quality peer review is a necessary ingredient for this to occur. It is a good analogy. This is not to mean that peer review is infallible, and there are many cases in which it has helped impede publication of truly innovative work, including several studies that have subsequently delivered Nobel prizes (Campanario 2009). As such, it has been claimed that peer review ‘favors unadventurous nibblings at the margin of truth rather than quantum leaps’ (Lock 1985). Ecology is not immune from this problem; the ‘why is the world green’ paper by Hairston, Smith and Slobodkin (1960), arguably the most influential publication in trophic ecology in the past 60 years, was first rejected by Ecology (Schoener 1989). Nevertheless, peer review overall does more good than bad, and so long as that is the case, its contribution to the evolutionary process that Hochberg (2014) describes should be positive overall. Erosion of the quality of peer review, when combined with the shortcomings that the peer review process already has, will inevitably retard this evolutionary process. Hochberg (2014) also makes the case that overexploitation of reviewers (i.e., ‘tragedy of the reviewer commons’) is likely to reduce the effectiveness of reviewers which will then push overall scientific quality downwards. He then identifies three mechanisms that should counter this effect. However, I suggest that Hochberg overlooks an important issue contributing to reviewer exploitation, and that until this is resolved by the scientific community to some satisfaction, declining effectiveness of the peer-review process in maintaining scientific quality is inevitable. The issue in question relates to journal ‘impact factors’ (hereafter IFs) and the obsession that many journals and scientists have with them. This appears to have contributed to many ecological journals implementing ever-decreasing acceptance rates (now 10–20% for most of the main ecological journals), on the belief that being more selective and publishing only work that is likely to be generously cited will elevate their impact factor relative to that of competing journals. It has also contributed to scientists flooding high-IF journals with submissions. Inevitably many of these manuscripts will be submitted to three or four (or more) journals over time before publication, and may consume the time of many reviewers and editors in the process (not to mention greatly delaying communication of the science to those who might find it useful). This may not always be due to the authors aiming too high—given that the fate of any manuscript following submission to any highly selective journal is partly determined by stochastic factors (i.e., based on whose desk it happens to lands on), an author of even an excellent paper might need to submit to two or ","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70234676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The tragedy of the tragedy of the commons","authors":"M. Hochberg, James H. Brown","doi":"10.4033/IEE.2014.7.19.E","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.19.E","url":null,"abstract":"Humanity is playing out the tragedy of the commons on a global scale. At present rates, each individual added to the global human population will annually consume about 0.5 tonnes of cereal grain, 0.05 tonnes of meat or fish, 1 million litres of water, 0.3 tonnes of wood, 4.5 barrels of oil, 0.3 tonnes of copper, and 0.2 tonnes of phosphate fertilizer, and each one will release about 5 tonnes of CO2 and 4 tonnes of solid and liquid waste into the environment. If these numbers seem large, multiply each of them by 2,000,000,000 to estimate the additional consumption by 2050 when the global population has grown from its current 7.1 billion to over 9 billion (UN 2010). The resulting numbers are almost incomprehensible. The bottom line is that enormous quantities of natural resources will need to be extracted from the earth to support projected population growth (e.g., Brown et al. 2011). Additional quantities, especially of energy and metals, will be required to increase overall standards of living and to reduce poverty and disease, especially in developing countries. How can these resources be obtained, and at what cost to the environment and biodiversity of the planet (e.g., Wackernagel and Rees 1998, IPCC 2007)? Several approaches have addressed these issues: limits to food supplies (e.g., Pauly et al. 2005, Godfray et al. 2010, Foley et al. 2011, Tilman et al. 2012), supply and distribution of fresh water (Gleick and Palaniappan 2010), availability of alternative sources of energy (e.g., Hall and Klitgaard 2011), and threats from chronic and pandemic diseases (Heymann 2003, Osterholm 2005). A few efforts been made to provide more comprehensive analyses of multiple limiting factors, perhaps most notably the ecological footprint approach of the group at the University of British Columbia (http://www.footprintnetwork.org/en/ index.php/GFN/) and the planetary boundaries analyses of Stockholm Resilience Center (Rockström et al. 2009). Nevertheless, most of the attention has been piece-meal—focused on specific problems such as greenhouse gas emissions, climate change, and the outbreak of the H1N1 influenza.","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4033/IEE.2014.7.19.E","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70234760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What makes a topic “relevant” to journal editors?","authors":"S. Palacio, A. Escudero","doi":"10.4033/IEE.2014.7.18.F","DOIUrl":"https://doi.org/10.4033/IEE.2014.7.18.F","url":null,"abstract":"Suitability of a paper for a specific journal is often based on an evanescent concept: the relevance of the topic covered to managing editors. Pressure for publishing has never been so high. An academic’s future position, funding, and prestige all depend on the quantity of papers published, their quality (or that of the journal in which they are published) and the number of citations they receive. Similarly, scientific journals face increasing pressure to boost their impact factor and climb up the journal rank of their respective categories. Most journals (particularly those with the highest impact factors) receive an overwhelming number of manuscripts that exceeds their capacity for peer-review. Consequently, editors often base a decision to accept or reject a manuscript on the interest of papers for the readers of their journal. The first decision that editors face is whether to send a paper for peer review. Editorial rejections prior to peer review reduce the burden on the already saturated community of reviewers and may save time for authors who can readily submit their paper to a different journal (Cooke and Lapointe 2012). However, they also increase the rejection rate per author. Indeed, editorial rejections are an important source of frustration for authors, who have to spend tedious time in reformatting their papers without any reward in terms of feedback, because these rejections are normally poorly justified and based on very general statements. Leaving aside issues on the fit of papers to the journal scope and aims (which should be clearly explained in the journal web site, (Cooke and Lapointe 2012)), editorial decisions are mostly based on this ethereal idea of the perceived relevance of the topic covered by deciding editors. Hidden by anonymity (in pre peer-review rejections, the name of the subject editor is frequently not revealed) and justified by a baseless “lack of space” in the journal (when most journals are online and available space has become almost infinite (Aarssen 2012, Wardle 2012)), editors are empowered to reject papers, openly disregarding the scientific quality of the contribution in favour of an alleged lack of interest or the consideration that the manuscript is of relevance only for a narrow community. But editors, by their very nature, must be generalists, even in specialized journals. This means they are frequently not familiar with the field of the paper they are evaluating. Consequently, a decision based on the relevance of the paper to their audience may not be straightforward, particularly without the expert views of peers. Should this type of decision be left in the hands of just one person? We argue here that assessments from a sole individual, frequently not familiar with the field of the paper, may be thematically and/or geographically biased, and therefore, lead to erroneous conclusions, preventing the advance of knowledge. Ideally, a relevant paper would be one that has the capacity to move the field","PeriodicalId":42755,"journal":{"name":"Ideas in Ecology and Evolution","volume":"7 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70234688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}