Making environmental DNA count

The arc of reception for a new technology or method – like the reception of new information itself – can pass through predictable stages, with audiences’ responses evolving from ‘I don't believe it’, through ‘well, maybe’ to ‘yes, everyone knows that’ to, finally, ‘old news’. The idea that one can sample a volume of water, sequence DNA out of it, and report what species are living nearby has experienced roughly this series of responses among biologists, beginning with the microbial biologists who developed genetic techniques to reveal the unseen microbiome. ‘Macrobial’ biologists and ecologists – those accustomed to dealing with species they can see and count – have been slower to adopt such molecular survey techniques, in part because of the uncertain relationship between the number of recovered DNA sequences and the abundance of whole organisms in the sampled environment. In this issue of Molecular Ecology Resources, Evans et al. ( 2015 ) quantify this relationship for a suite of nine vertebrate species consisting of eight fish and one amphibian. Having detected all of the species present with a molecular toolbox of six primer sets, they consistently find DNA abundances are associated with species’ biomasses. The strength and slope of this association vary for each species and each primer set – further evidence that there is no universal parameter linking recovered DNA to species abundance – but Evans and colleagues take a significant step towards being able to answer the next question audiences tend to ask: ‘Yes, but how many are there?’     

The Effects of Hydrostatic Pressure on Living Aquatic Organisms V. Eurybiotic Environmental Capacity as a Factor in High Pressure Tolerance

Study on the total spectrum of organisms (72 species) subjected to hydrostatic pressure as of this date allows one to established categories of pressure tolerance (resistance): Extremely high – eurybiotic forms (1000–1200 atm), High – marine littoral, planktonic, freshwater (600–1000 atm), Moderate – marine littoral, planktonic, freshwater (400–600 atm), Low – planktonic, freshwater (100–300 atm), Extremely low – planktonic, freshwater (0–100 atm). The average pressure tolerance of marine littoral species is higher than that of planktonic species but not significantly different from freshwater species. Eurybiotic species which are not marine seem to show the highest pressure tolerance.     

The evolution and ecology of benign tumors

Tumors are usually classified into two main categories – benign or malignant, with much more attention being devoted to the second category given that they are usually associated with more severe health issues (i.e., metastatic cancers). Here, we argue that the mechanistic distinction between benign and malignant tumors has narrowed our understanding of neoplastic processes. This review provides the first comprehensive discussion of benign tumors in the context of their evolution and ecology as well as interactions with their hosts. We compare the genetic and epigenetic profiles, cellular activities, and the involvement of viruses in benign and malignant tumors. We also address the impact of intra-tumoral cell composition and its relationship with the tumoral microenvironment. Lastly, we explore the differences in the distribution of benign and malignant neoplasia across the tree of life and provide examples on how benign tumors can also affect individual fitness and consequently the evolutionary trajectories of populations and species. Overall, our goal is to bring attention to the non-cancerous manifestations of tumors, at different scales, and to stimulate research on the evolutionary ecology of host–tumor interactions on a broader scale. Ultimately, we suggest that a better appreciation of the differences and similarities between benign and malignant tumors is fundamental to our understanding of malignancy both at mechanistic and evolutionary levels.     

‘Bridges to cash’: channelling agency in mobile money

Encountered by mobile money professionals – industry and philanthropic actors seeking to bring mobile phone‐enabled financial products to poor people in the ‘developing world’ – the authors move together with new collaborators to inquire into a problem they had been grappling with for some time. This is the problem of agency; specifically, the agency of ‘mobile money agents’, the people ‘on the ground’ or ‘in the field’ who form a crucial function in permitting others to put cash into an electronic money transfer system and pull cash out of it. These ‘human ATMs’ or ‘bridges to cash’ become the object of analytical scrutiny for mobile money experts and anthropologists. This article takes that analytical scrutiny – and not mobile money agents themselves – as its object. It seeks to understand how ‘agency’ inflects debates over money, its meaning and its pragmatics, and its transformation in new communicative infrastructures, and how it might inform anthropology and political struggles over money and payment.     

The Chinese family as instituted fantasy: or,rescuing kinship imaginaries from the ‘symbolic’

This article revisits well‐travelled ethnographic portrayals of traditional Chinese family dynamics to draw attention to desire as a product of family life and to how crucial elements of family organization and ideology can be understood, in turn, as effects of desire – that is, as instituted fantasies. Although my case in point is the Chinese family, the analysis addresses the category ‘family’ cross‐culturally. In any of its variations, the ‘family’ exists at two synergistically implicated levels: first, it comprises an important part of the reality into which individuals are socialized; second, it embodies in instituted form individuals' attempts to realize – to bring into being – social arrangements as they would like them to be. In the Chinese case, at least two ironies are embedded in this synergy. First, women are primary producers and reproducers of the family in the ‘real world’, despite the fact that patriliny as ‘instituted fantasy’ downplays or veils their agency. Second, the normative subordination of the son to a patriarchal father, expressed and mediated through institutions including ancestor worship and valorization of filial piety, veils a valorizing of the son as agent or protagonist of filial action. Although ultimately unrealizable, patrilineal and familial fantasies animate Chinese family life and are thus an important constituent of Chinese realities. To these ends the analysis re‐purposes ‘the symbolic’ and ‘imaginaries’, categories widely employed in contemporary gender studies and social theory, arguing that understanding kinship enjoins incorporating desire's role both in defining institutions and in motivating their creators.     

Incorporating evolutionary processes into conservation planning using species distribution data: a case study with the western Mediterranean herpetofauna

Aim To incorporate evolutionary processes into conservation planning using species distribution patterns and environmental gradients as surrogates for genetic diversity. Location Western Mediterranean Basin. Methods Distributions of 154 herpetological species were predicted using maximum entropy models, and groups of significantly co‐occurring species (biotic elements) were identified. Environmental gradients were characterized for the complete area and for the area covered by each biotic element, by performing a principal component analysis on the data matrix composed of nine environmental variables. The first two principal component analysis axes were classified into four categories each, and those categories were combined with each other resulting in an environmental classification with 16 categories. To identify priority conservation areas, biotic elements and environmental categories were used as surrogates for the neutral and adaptive components of genetic diversity, respectively. Priority areas for conservation were identified under three scenarios: (1) setting targets for species only; (2) setting targets for species and for each environmental category of the overall area; and (3) setting targets for each species and for each environmental category within each biotic element. Results Nine biotic elements were identified – four for the amphibians and five for the reptiles. Priority areas identified in the three scenarios were similar in terms of amount of area selected, but exhibited low spatial agreement. Main conclusions Prioritization exercises that integrate surrogates for evolutionary processes can deliver spatial priorities that are fairly different to those where only species representation is considered. While new methods are emerging to incorporate molecular data in conservation prioritization, it is unlikely to be enough data for enough taxa for this to be feasible in many regions. We develop an approach using surrogates for both the neutral and adaptive components of genetic diversity that may enhance biodiversity persistence and representation when molecular data are not available or geographically comprehensive.     

CMA restricted to mammals and birds: myth or reality?

Chaperone-mediated autophagy (CMA) is a major pathway of lysosomal proteolysis essential for the control of intermediary metabolism. So far, the absence of any identifiable LAMP2A – a necessary and limiting protein for CMA – outside of the tetrapod clade, led to the paradigm that this cellular function was (presumably) restricted to mammals and birds. However, after we identified expressed sequences displaying high sequence homology with the mammalian LAMP2A in several fish species, our findings challenge that view and suggest that CMA likely appeared much earlier during evolution than initially thought. Hence, our results do not only shed an entirely new light on the evolution of CMA, but also bring new perspectives on the possible use of complementary genetic models, such as zebrafish or medaka for studying CMA function from a comparative angle/view.     

Conservation biogeography of the US–Mexico border: a transcontinental risk assessment of barriers to animal dispersal

Aim Humans have dramatically transformed landscapes along the US–Mexico border. We aim to assess the risk of barriers that may significantly impede animal migrations within this ecologically sensitive region. Location United States and Mexico. Methods We examined the intersection of current and possible future barriers along the border with the geographic ranges of 313 amphibian, reptile and non‐volant mammal species. We considered the areas of intensive human land use and ～ 600 km of pedestrian fence as current barriers along the border. We evaluated the impacts of two scenarios of dispersal barriers – continuation of existing and construction of new barriers – and identified species vulnerable to global and local extinction. Results Among the species most at risk from current barriers are four species listed as threatened globally or by both nations, 23 species for which the larger of their two national subranges is < 10⁵ km² and 29 species whose ranges cross the border only marginally. Three border regions, California, Madrean archipelago and Gulf coast, emerge as being of particular concern. These regions are characterized by high overall species richness and high richness of species at risk from existing barriers and from construction of potential new barriers. Main conclusions New barriers along the border would increase the number of species at risk, especially in the three identified regions, which should be prioritized for mitigation of the impacts of current barriers. The species we identified as being potentially at risk merit further study to determine impacts of border dispersal barriers.     

Ecology and Biodiversity of Coral Reef Polychaetes of Guam and Saipan,Mariana Islands.

Polychaetes collected from coral reefs and other coastal habitats on Guam and Saipan, and information from published studies bring the known number of species from these two islands to 101 and 15, respectively. Sediment and rock dwelling species collected, and those previously recorded, belong to 25 families. Polychaete assemblages are compared on the basis of species richness, genera in common, and trophic categories, with other West Pacific, Hawaiian and East Indian Ocean locations. Polychaetes from Guam are similar to those on reef flats of Hawaii, Enewetak, and Indonesia in faunal composition and density. Despite the limitations in comparable collecting effort and quantitative analyses for some of the areas, these coral reefs have similar complements of families and genera present, and proportions of four trophic categories.     

Einwanderungsrouten nach Mitteleuropa

Butterflies – who is coming, who is going? Immigration routes to Central Europe The majority of butterflies and burnet moths distributed in Central Europe today results from postglacial colonisation of this region mostly from expansions out of the well known Mediterranean refuge areas. The study region was mostly colonised west or east of the Alps, which represent a strong dispersal obstacle. Species being widespread under glacial conditions in Central Europe have retreated under the warm conditions of the Postglacial to the high mountain systems or the Arctic. Therefore, they are mostly restricted to the high altitudes of the Alps in Western Central Europe. Nevertheless, some species have even survived in lowland areas of Central Europe during glacial and inter‐/postglacial conditions, but these species are either better adapted to glacial or to inter‐/postglacial conditions.     

North Atlantic marine communities through time

How and why ecological communities change their species membership over time and space is a central issue in ecology and evolution. Phylogeographic approaches based on animal mitochondrial DNA sequences have been important for revealing historical patterns of individual species and can provide qualitative comparisons among species. Exciting new methods, particularly implementing approximate Bayesian computation (ABC – Beaumont et al. 2002 ), now allow model‐based quantitative comparisons among species and permit the probabilistic exploration of alternative community‐level hypotheses (see review by Hickerson et al. 2010 ). In this issue of Molecular Ecology, Ilves et al. (2010) use an ABC approach to bring fresh insights into the well‐studied question of how North Atlantic coastal species contracted and expanded their ranges in response to late Pleistocene/Holocene climate fluctuations.     

Emerging niche clustering results from both competition and predation

Understanding species coexistence has been a central question in ecology for decades, and the notion that competing species need to differ in their ecological niche for stable coexistence has dominated. Recent theoretical and empirical work suggests differently. Species can also escape competitive exclusion by being similar, leading to clusters of species with similar traits. This theory has so far only been explored under competition. By combining mathematical and numerical analyses, we reveal that competition and predation are equally capable to promote clusters of similar species in prey–predator communities, their relative importance being modulated by resource availability. We further show that predation has a stabilizing effect on clustering patterns, making the clusters more diverse. Our results merge different ecological theories and bring new light to the emergent neutrality theory by adding the perspective of trophic interactions. These results open new perspectives to the study of trait distributions in ecological interaction networks.     

落叶松树种的体细胞胚胎发生与规模化技术体系

植物体细胞胚胎发生技术是植物体细胞在人为可控条件下通过与合子胚胎发生类似的途径 ,发育出新个体的再生技术 ,自问世以来 ,已被广泛用于生命科学领域。对落叶松及其杂种胚性细胞系的大规模增殖培养、原胚发育状态、体细胞胚成苗和专用生物反应器技术体系的建立以及其应用、展望等方面进行了探讨 ,表明落叶松体细胞胚胎发生过程中专用生物反应器技术体系的完善与建立迫在眉睫 ,并将为现代林木育种与繁殖工程及生命科学相关学科的发展带来重要影响 。     

Rhinacanthus spiciformis,a new species of Acanthaceae from northern Vietnam

Rhinacanthus spiciformis Y. F. Deng, Z. L. Lin & D. V. Hai, a new species from northern Vietnam previously misidentified as R. calcaratus is described and illustrated. This new species differs from all other Asian species of Rhinacanthus in the inflorescence being unbranched or comprised of trifurcate-branched spikes, and the lower lip of corolla with conspicuous purple stripes near throat and on lobes. The pollen morphology and chromosome number are presented. It is proposed to be accessed as Least Concern (LC) according to the IUCN categories and criteria.     

Quality control in molecular genetic testing

DNA-based testing for genetic diseases has developed from nothing into a principal part of laboratory medicine over the past 15 years. In the rush to bring these powerful new technologies into medical use, issues of quality have not always been given sufficient attention. Efforts are now being made to assess the quality of the output of genetic testing laboratories, and the results show that there is room for improvement.     

Static and dynamic approaches to landscape heterogeneity in the Hungarian forest‐steppe zone

Abstract. This paper describes the successional status of the vegetation in a clear‐felled dry oak woodland at the edge of the Hungarian forest‐steppe zone on the basis of a vegetation map. Due to a varied geomorphology of the colline landscape several so‐called landscape units can be distinguished. The patchwork on the vegetation map is evaluated using several, morphology‐based attributes (static morphological indices) traditionally applied in landscape ecology. In the ca. 100 years that elapsed since forest clear‐cut, xeric grassland species and steppe elements became more abundant and the former xeromesophilous vegetation – containing even some woodland components – is slowly turning into xeric grassland communities. The vegetation units mapped can be arranged into a hypothetical succession scheme in which successional distances (the number of steps between two stages) are determined. Based on the distances thus obtained, a new dynamic morphological index is introduced. This is applied to each landscape unit for the dynamic evaluation of successional vegetation, its results being compared with those obtained by static morphological indices.     

Translocation for conservation: Neonates are less suitable than adults

Animal behaviour can affect the outcome of conservation translocations. It is important to understand the behaviour of the species being considered for translocation and how its behaviour varies over life stages. There may be uncertainty about what life stages are best as founders for release back into wild populations. A technique called head‐starting whereby juvenile life stages are raised in captivity and then released is one potential pre‐release strategy. However, juveniles of many species have a dispersive role in the life cycle, potentially raising difficulties for establishing new populations due to dispersal from the intended habitat following release. For this study, we compared aspects of the behaviour of captive adult and neonate pygmy bluetongue lizards (Tiliqua adelaidensis) – an endangered species for which translocation is likely to be an important management strategy – to determine if neonate behavioural characteristics are appropriate for their translocation. We filmed adult and neonate pygmy bluetongue lizards and compared their behaviour. We also filmed adults over an activity season to compare seasonal behaviour. Behavioural parameters measured included basking time, burrow exits, burrows occupied and walking the perimeter wall. Neonates basked significantly more than adults in summer and autumn. Neonates are likely to be basking more than adults because they are in a stage of rapid growth and need to gain body mass before the winter inactivity period. Neonates exited burrows more often than adults and used a greater number of burrows. These results indicate neonate lizards are actively exploring their habitat. Neonates are unlikely to be as suitable for translocation as they are actively moving about and more likely to be predated upon or disperse from the translocation site. Our finding can be applied to other species that have active juvenile life stages and are at particular risk of predation due to their small size.     

Known knowns and unknowns in biology

Here we present a knowledge‐data framework based on the politico‐military statement by Donald Rumsfeld (below) which has, we believe, direct relevance to ecological conservation. Ecological examples of four of the identified categories are provided with discussion of the conservation risks to a species through knowledge or data loss and movement through the categories. We show that so‐called known knowns in terms of global biodiversity are not as accurately known as thought, despite 500 years or more of world‐wide collecting and recording of eukaryotic species. In addition, as fast as new species, living or fossil, are discovered (unknown unknowns), some of which have revolutionised concepts about the biology of particular taxa, meanwhile, sadly other living species are being extirpated, or are assumed to be so (unknown knowns). These often have a high probability of ultimately being rediscovered, especially if small and/or living in remote, under‐sampled regions. Furthermore, we suggest that in some cases it may be possible to predict the existence of known species in new habitats, or the existence of unknown co‐evolved animal species (known unknowns). We discuss how technological advances (e.g. molecular markers and DNA sequencing) are inflating current estimates of biodiversity by identifying the existence of cryptic species. We believe the knowledge‐data matrix provides another tool for conservation practitioners to focus data collection on bridging knowledge gaps for more effective conservation outcomes.     

Microbial decolourisation and degradation of textile dyes

Dyes and dyestuffs find use in a wide range of industries but are of primary importance to textile manufacturing. Wastewater from the textile industry can contain a variety of polluting substances including dyes. Increasingly, environmental legislation is being imposed to control the release of dyes, in particular azo-based compounds, into the environment. The ability of microorganisms to decolourise and metabolise dyes has long been known, and the use of bioremediation based technologies for treating textile wastewater has attracted interest. Within this review, we investigate the mechanisms by which diverse categories of microorganisms, such as the white-rot fungi and anaerobic bacterial consortia, bring about the degradation of dyestuffs.     

丽叶蝉属一新种和一中国新记录种（同翅目：叶蝉科：离脉叶蝉亚科）

丽叶蝉属（ Ｃａｌｏｄｉａ Ｎｉｅｌｓｏｎ） 隶属于叶蝉科（ Ｃｉｃａｄｅｌｌｉｄａｅ）、离脉叶蝉亚科（ Ｃｏｅｌｉｄｉｉｎａｅ）、离脉叶蝉族（ Ｃｏｅｌｉｄｉｉｎｉ）,由 Ｎｉｅｌｓｏｎ 建立于１９８２年。它是离脉叶蝉族中较大的１个属,现已知５７种,分布于整个东洋区。国内张雅林于１９９４年在其专著《中国离脉叶蝉分类》一书中系统描述了中国丽叶蝉属１９种。本文记述１新种和１中国新记录种。至此全世界已知丽叶蝉属５８种,中国已知２１种。１． 叉突丽叶蝉 Ｃａｌｏｄｉａ ｂｉｆｕｒｃａｔａ, 新种（图１）♂：体长８．５ｍ ｍ 。正模♂：贵州宽阔水,１９８４－ Ⅷ－ ７,李子忠采。模式标本存放于安徽农业大学植保系。本种雄性外生殖器特征相似于粗突丽叶蝉 Ｃａｌｏｄｉａ ｒｏｂｕｓｔａ Ｎｉｅｌｓｏｎ,但本种阳基侧突长,亚端部分二叉,而后者阳基侧突粗壮,亚端部扩大,不分叉。２． 刺板丽叶蝉 Ｃａｌｏｄｉａ ｂｉｓｐｉｎｏｓａ Ｎｉｅｌｓｏｎ, 中国新记录（图２）♂：体长７．８ｍ ｍ ～８．０ｍ ｍ 。分布：泰国：中国（云南）。该种为 Ｎｉｅｌｓｏｎ （１９８２） 根据泰国１雄虫标本建立的新种,作者首次发现中国云南亦有其分布。本种雄性外生殖器特征相似