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Predicting the fate of eDNA in the environment and implications for studying biodiversity 预测环境中eDNA的命运及其对生物多样性研究的意义
Pub Date : 2019-11-20 DOI: 10.1098/rspb.2019.1409
J. B. Harrison, J. Sunday, S. Rogers
Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.
环境DNA (eDNA)的应用正在改变通过从环境样本中收集DNA的存在、位置和丰度来表征水生生物多样性的标准。由于eDNA研究使用DNA片段作为生物体存在的代表,因此需要考虑采集eDNA的复杂动态环境的生态特性,以便进行准确的生物学解释。在这篇综述中,我们讨论了不同的环境对eDNA在生物体和收集过程中所经历的主要过程的作用,包括脱落、腐烂和运输。我们专注于对这些过程的机制理解,并强调如何发展衰变和运输模型,以更准确和可靠地预测eDNA的命运。最后,我们对eDNA研究人员和从业者提出了五项建议,以推进当前的最佳实践,并支持eDNA时空持久性的未来模型。
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引用次数: 230
Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses 变化的环境和遗传变异:近亲繁殖的自然变异不会损害短期的生理反应
Pub Date : 2019-11-20 DOI: 10.1098/rspb.2019.2109
James Buckley, Rónán Daly, C. Cobbold, Karl E. V. Burgess, B. Mable
Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce their long-term evolutionary potential. However, appropriate short-term plastic responses to new environmental conditions might not require high levels of standing genetic variation. In this study, we tested whether mating system variation among populations, and associated changes in genetic variability, affected short-term responses to environmental challenges. We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a perennial plant, Arabidopsis lyrata, under constant growth chamber conditions and an outdoor common garden environment outside its native range. We found no effect of inbreeding on survival, flowering phenology or short-term physiological responses. Specifically, naturally occurring inbreeding had no significant effects on the plasticity of metabolome profiles, using either multivariate approaches or analysis of variation in individual metabolites, with inbreeding populations showing similar physiological responses to outbreeding populations over time in both growing environments. We conclude that low genetic diversity in naturally inbred populations may not always compromise fitness or short-term physiological capacity to respond to environmental change, which could help to explain the global success of selfing mating strategies.
尽管遗传多样性降低,但自交植物谱系在广泛的环境中惊人地广泛和成功,这被预测会降低它们的长期进化潜力。然而,对新环境条件的适当的短期可塑性反应可能不需要高水平的常备遗传变异。在这项研究中,我们测试了种群间交配制度的变化以及相关的遗传变异是否会影响对环境挑战的短期反应。本研究比较了多年生植物拟南芥(Arabidopsis lyrata)在恒定生长室条件下和室外普通花园环境下自然远交(遗传多样性)和近交(遗传退化)种群的相对适应度和代谢组学特征。我们没有发现近亲繁殖对存活、开花物候或短期生理反应有影响。具体而言,通过多变量方法或个体代谢物变异分析,自然发生的近亲繁殖对代谢组谱的可塑性没有显著影响,随着时间的推移,在两种生长环境中,近亲繁殖群体表现出与近亲繁殖群体相似的生理反应。我们的结论是,自然近交种群的低遗传多样性可能并不总是损害适应性或短期生理能力,以应对环境变化,这有助于解释自交交配策略在全球范围内的成功。
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引用次数: 7
A molecular war: convergent and ontogenetic evidence for adaptive host manipulation in related parasites infecting divergent hosts 一场分子战争:在感染不同宿主的相关寄生虫中适应性宿主操纵的趋同和个体发生证据
Pub Date : 2019-11-20 DOI: 10.1098/rspb.2019.1827
R. Herbison, S. Evans, Jean‐François Doherty, Michael Algie, T. Kleffmann, R. Poulin
Mermithids (phylum Nematoda) and hairworms (phylum Nematomorpha) somehow drive their arthropod hosts into water, which is essential for the worms' survival after egression. The mechanisms behind this behavioural change have been investigated in hairworms, but not in mermithids. Establishing a similar mechanistic basis for host behavioural change between these two distantly related parasitic groups would provide strong convergent evidence for adaptive manipulation and insight into how these parasites modify and/or create behaviour. Here, we search for this convergence, and also contrast changes in physiology between hosts infected with immature and mature mermithids to provide the first ontogenetic evidence for adaptive manipulation by disentangling host response and pathology from the parasite's apparent manipulative effects. We used SWATH-mass spectrometry on brains of Forficula auricularia (earwig) and Bellorchestia quoyana (sandhopper), infected with the mermithids Mermis nigrescens and Thaumamermis zealandica, respectively, at both immature and mature stages of infection, to quantify proteomic changes resulting from mermithid infection. Across both hosts (and hairworm-infected hosts, from earlier studies), the general function of dysregulated proteins was conserved. Proteins involved in energy generation/mobilization were dysregulated, corroborating reports of erratic/hyperactive behaviour in infected hosts. Dysregulated proteins involved in axon/dendrite and synapse modulation were also common to all hosts, suggesting neuronal manipulation is involved in inducing positive hydrotaxis. Furthermore, downregulation of CamKII and associated proteins suggest manipulation of memory also contributes to the behavioural shift.
丝虫(线虫门)和毛虫(线虫门)以某种方式将它们的节肢动物宿主驱入水中,这对蠕虫在离开后的生存至关重要。这种行为变化背后的机制已经在毛虫中进行了研究,但在梭子虫中还没有。在这两个远亲寄生群体之间建立宿主行为改变的类似机制基础,将为适应性操纵和深入了解这些寄生虫如何改变和/或创造行为提供强有力的趋同证据。在这里,我们寻找这种收敛性,并对比了未成熟和成熟梭子虫感染宿主之间的生理变化,通过将宿主反应和病理与寄生虫的明显操纵效应分离开来,为适应性操纵提供第一个个体发生证据。本研究分别用swath -质谱法对感染了mermithids Mermis nigrescens和Thaumamermis zealandica的土耳Forficula auricularia和Bellorchestia quoyana在未成熟和成熟阶段的大脑进行了分析,以量化mermithids感染引起的蛋白质组学变化。在两种宿主(以及早期研究中发现的被毛虫感染的宿主)中,失调蛋白的一般功能是保守的。参与能量产生/动员的蛋白质失调,证实了感染宿主不稳定/过度活跃行为的报告。参与轴突/树突和突触调节的失调蛋白在所有宿主中也很常见,这表明神经元操纵参与了诱导正向疏水性。此外,CamKII和相关蛋白的下调表明,对记忆的操纵也有助于行为转变。
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引用次数: 14
Cerebral blood flow rates in recent great apes are greater than in Australopithecus species that had equal or larger brains 现代类人猿的脑血流量比拥有同等或更大大脑的南方古猿要大
Pub Date : 2019-11-13 DOI: 10.1098/rspb.2019.2208
R. Seymour, Vanya Bosiocic, Edward P. Snelling, Prince C. Chikezie, Qiaohui Hu, Thomas J. Nelson, B. Zipfel, C. V. Miller
Brain metabolic rate (MR) is linked mainly to the cost of synaptic activity, so may be a better correlate of cognitive ability than brain size alone. Among primates, the sizes of arterial foramina in recent and fossil skulls can be used to evaluate brain blood flow rate, which is proportional to brain MR. We use this approach to calculate flow rate in the internal carotid arteries (Q˙ICA), which supply most of the primate cerebrum. Q˙ICA is up to two times higher in recent gorillas, chimpanzees and orangutans compared with 3-million-year-old australopithecine human relatives, which had equal or larger brains. The scaling relationships between Q˙ICA and brain volume (Vbr) show exponents of 1.03 across 44 species of living haplorhine primates and 1.41 across 12 species of fossil hominins. Thus, the evolutionary trajectory for brain perfusion is much steeper among ancestral hominins than would be predicted from living primates. Between 4.4-million-year-old Ardipithecus and Homo sapiens, Vbr increased 4.7-fold, but Q˙ICA increased 9.3-fold, indicating an approximate doubling of metabolic intensity of brain tissue. By contrast, Q˙ICA is proportional to Vbr among haplorhine primates, suggesting a constant volume-specific brain MR.
脑代谢率(MR)主要与突触活动的成本有关,因此可能比脑大小单独与认知能力有更好的关联。在灵长类动物中,最近和化石头骨的动脉孔大小可以用来评估脑血流量,这与脑mr成正比。我们使用这种方法来计算内颈动脉的流量(Q˙ICA),这是灵长类动物大脑的主要供血来源。与300万年前的人类近亲南方古猿相比,最近的大猩猩、黑猩猩和猩猩的Q˙ICA高达两倍,后者的大脑大小相同或更大。Q˙ICA与脑容量(Vbr)的比例关系显示,44种单灵长类动物的指数为1.03,12种古人类的指数为1.41。因此,人类祖先脑灌注的进化轨迹比现存灵长类动物预测的要陡峭得多。在440万年前的地猿和智人之间,Vbr增加了4.7倍,但Q˙ICA增加了9.3倍,这表明脑组织的代谢强度大约增加了一倍。相比之下,单灵长类动物的Q˙ICA与Vbr成正比,表明大脑MR是恒定的体积特异性。
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引用次数: 9
Intraspecific male combat behaviour predicts morphology of cervical vertebrae in ruminant mammals 种内雄性战斗行为预测反刍哺乳动物颈椎形态
Pub Date : 2019-11-13 DOI: 10.1098/rspb.2019.2199
Abby Vander Linden, E. Dumont
Cranial weapons of all shapes and sizes are common throughout the animal kingdom and are frequently accompanied by the evolution of additional traits that enhance the use of those weapons. Bovids (cattle, sheep, goats, antelope) and cervids (deer) within the mammal clade Ruminantia are particularly well known for their distinct and varied cranial appendages in the form of horns and antlers, which are used as weapons in intraspecific combat between males for access to mates. Combat in these species takes many forms, including head-on collisions (ramming); stabbing an opponent's head or body with horn tips (stabbing); rearing and clashing downwards with horns (fencing); or interlocking antlers or horns while vigorously pushing and twisting (wrestling). Some aspects of weapon and skull morphology have been linked to combat behaviours in bovid and cervid species, but the contribution of postcranial structures that support these weapons, such as the neck, has not been explored. To investigate the role of the neck in intraspecific combat, we quantified biomechanically relevant linear variables of the cervical vertebrae (C1–C7) from males and females of 55 ruminant species. We then used phylogenetic generalized least-squares regression to assess differences among species that display primarily ramming, stabbing, fencing and wrestling combat styles. In males, we found that wrestlers have longer vertebral centra and longer neural spines than rammers, stabbers or fencers, while rammers have shorter and wider centra and taller neural spine lever arms. These results suggest a supportive role for the cervical vertebrae in resisting forces generated by male–male combat in ruminant mammals and indicate that evolutionary forces influencing cranial weapons also play a role in shaping the supporting anatomical structures.
各种形状和大小的头盖骨武器在动物王国中很常见,并且经常伴随着其他特征的进化,从而增强了这些武器的使用。反刍动物分支中的牛科动物(牛、绵羊、山羊、羚羊)和鹿科动物(鹿)以其独特而多样的头颅附属物而闻名,这些附属物以角和角的形式出现,在雄性之间的种内战斗中被用作武器,以获得配偶。这些物种的战斗形式多种多样,包括正面碰撞(冲撞);用角尖刺对方的头部或身体(刺);直立的,用角向下碰撞(围栏);或在大力推动和扭转(摔跤)时将鹿角或角联锁。武器和头骨形态的某些方面与牛科和子科物种的战斗行为有关,但支持这些武器的后颅结构(如颈部)的贡献尚未得到探索。为了研究颈部在种内战斗中的作用,我们量化了55种反刍动物雄性和雌性颈椎(C1-C7)的生物力学相关线性变量。然后,我们使用系统发育广义最小二乘回归来评估主要表现为撞击,刺伤,击剑和摔跤战斗风格的物种之间的差异。在男性中,我们发现摔跤手比锤击手、刺击手或击剑手有更长的椎体中心和更长的神经棘,而锤击手的椎体中心更短更宽,神经棘杠杆臂更高。这些结果表明,在反刍哺乳动物中,颈椎在抵抗雄性-雄性战斗中产生的力量方面发挥了支持作用,并表明影响颅骨武器的进化力量也在形成支持解剖结构方面发挥了作用。
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引用次数: 12
Contrasting drivers of diversification rates on islands and continents across three passerine families 三个雀形目科在岛屿和大陆上多样化率的驱动因素对比
Pub Date : 2019-11-13 DOI: 10.1098/rspb.2019.1757
M. Conway, Brian J. Olsen
Diversification rates vary greatly among taxa. Understanding how species-specific traits influence speciation rates will help elucidate mechanisms driving biodiversity over broad spatio-temporal scales. Ecological specialization and range size are two hypothesized drivers of speciation rates, yet each mechanism predicts both increases and decreases in speciation. We constructed a continuous index of specialization using avian bill morphology to determine the relative effect of specialization and range size and shape on speciation rates across 559 species within the Emberizoidea superfamily, a morphologically diverse New World clade. We found a significant positive correlation between specialization and speciation rate and a negative correlation with range size. Only the effect of specialization persisted after removing island endemics, however, suggesting that ecological specialization is an important driver of diversity across large macroevolutionary scales, and the relative importance of specific drivers may differ between islands and continents.
不同分类群的多样化率差别很大。了解物种特异性性状如何影响物种形成率将有助于阐明在广泛的时空尺度上驱动生物多样性的机制。生态特化和范围大小是物种形成速率的两个假设驱动因素,但每种机制都预测物种形成的增加和减少。我们利用鸟类喙部形态构建了一个连续的特化指数,以确定特化、范围大小和形状对Emberizoidea超科559种物种形成率的相对影响。Emberizoidea超科是一个形态多样的新世界进化支。我们发现特化与物种形成率显著正相关,与范围大小负相关。然而,在去除岛屿特有物种后,只有专业化的影响持续存在,这表明生态专业化是大型宏观进化尺度上多样性的重要驱动因素,特定驱动因素的相对重要性在岛屿和大陆之间可能有所不同。
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引用次数: 10
Melanism protects alpine zooplankton from DNA damage caused by ultraviolet radiation 黑色素瘤保护高山浮游动物免受紫外线辐射造成的DNA损伤
Pub Date : 2019-11-06 DOI: 10.1098/rspb.2019.2075
C. K. Ulbing, Julia M. Muuse, Brooks E. Miner
Melanism is widely observed among animals, and is adaptive in various contexts for its thermoregulatory, camouflaging, mate-attraction or photoprotective properties. Many organisms exposed to ultraviolet radiation show increased fitness resulting from melanin pigmentation; this has been assumed to result in part from reduced UV-induced damage to DNA. However, to effectively test the hypothesis that melanin pigmentation reduces UV-induced DNA damage requires quantification of UV-specific DNA damage lesions following UV exposure under controlled conditions using individuals that vary in pigmentation intensity. We accomplished this using alpine genotypes of the freshwater microcrustacean Daphnia melanica, for which we quantified cyclobutane pyrimide dimers in DNA, a damage structure that can only be generated by UV exposure. For genotypes with carapace melanin pigmentation, we found that individuals with greater melanin content sustained lower levels of UV-induced DNA damage. Individuals with more melanin were also more likely to survive exposure to ecologically relevant levels of UV-B radiation. Parallel experiments with conspecific genotypes that lack carapace melanin pigmentation provide additional support for our conclusion that melanism protects individuals from UV-induced DNA damage. Finally, within-genotype comparisons with asexually produced clonal siblings demonstrate that melanin content influences DNA damage even among genetically identical individuals raised in the same environment.
黑化现象在动物中广泛存在,并因其温度调节、伪装、吸引配偶或光保护特性而适应于各种环境。许多暴露于紫外线辐射下的生物体显示出由于黑色素沉着而增加的适应性;这被认为部分是由于紫外线对DNA的损伤减少。然而,为了有效地验证黑色素色素沉着减少紫外线诱导的DNA损伤的假设,需要在控制条件下使用不同色素沉着强度的个体对紫外线照射后的紫外线特异性DNA损伤病变进行量化。我们使用淡水微甲壳类动物黑水蚤的高山基因型完成了这一任务,我们量化了DNA中的环丁烷嘧啶二聚体,这是一种只能由紫外线照射产生的损伤结构。对于具有甲壳黑色素色素沉着的基因型,我们发现黑色素含量较高的个体维持较低水平的紫外线诱导的DNA损伤。拥有更多黑色素的个体也更有可能在与生态相关的UV-B辐射水平下存活下来。对缺乏甲壳黑色素色素沉着的同种基因型进行的平行实验为我们的结论提供了额外的支持,即黑色素病可以保护个体免受紫外线诱导的DNA损伤。最后,与无性繁殖的克隆兄弟姐妹的基因型内比较表明,即使在相同环境中长大的基因相同的个体中,黑色素含量也会影响DNA损伤。
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引用次数: 7
Social wasps are effective biocontrol agents of key lepidopteran crop pests 群居黄蜂是对鳞翅目作物主要害虫的有效生物防治剂
Pub Date : 2019-11-06 DOI: 10.1098/rspb.2019.1676
R. Southon, O. Fernandes, F. Nascimento, S. Sumner
Biocontrol agents can help reduce pest populations as part of an integrated pest management scheme, with minimal environmental consequences. However, biocontrol agents are often non-native species and require significant infrastructure; overuse of single agents results in pest resistance. Native biocontrol agents are urgently required for more sustainable multi-faceted approaches to pest management. Social wasps are natural predators of lepidopteran pests, yet their viability as native biocontrol agents is largely unknown. Here, we provide evidence that the social paper wasp Polistes satan is a successful predator on the larvae of two economically important and resilient crop pests, the sugarcane borer Diatraea saccharalis (on sugarcane Saccharum spp.) and the fall armyworm Spodoptera frugiperda (on maize Zea mays); P. satan wasps significantly reduce crop pest damage. These results provide the much-needed baseline experimental evidence that social wasps have untapped potential as native biocontrol agents for sustainable crop production and food security.
作为综合虫害管理计划的一部分,生物防治剂可以帮助减少害虫种群,对环境的影响最小。然而,生物防治剂通常是非本地物种,需要大量的基础设施;过度使用单一药剂会产生害虫抗性。迫切需要本地生物防治剂,以实现更可持续的多方面害虫管理方法。群居黄蜂是鳞翅目害虫的天然捕食者,但其作为本土生物防治剂的可行性在很大程度上是未知的。本文提供的证据表明,社会纸蜂是甘蔗螟虫(Diatraea saccharalis)和玉米夜蛾(Spodoptera frugiperda)两种具有重要经济价值和抗灾能力的作物害虫幼虫的成功捕食者;撒旦小蜂能显著减少作物害虫的危害。这些结果提供了急需的基线实验证据,表明社会黄蜂作为可持续作物生产和粮食安全的原生生物防治剂具有未开发的潜力。
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引用次数: 29
Similar immediate costs of raising cuckoo and host chicks can hardly explain low levels of antiparasite defence in hosts. A Comment on: Samaš et al. (2018) 饲养布谷鸟和寄主雏鸟的直接成本相似,这很难解释寄主体内抗寄生虫防御水平低的原因。评论:samasi et al. (2018)
Pub Date : 2019-11-06 DOI: 10.1098/rspb.2018.2430
Canchao Yang, W. Liang, A. Møller
Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, People’s Republic of China Laboratoire d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Bâtiment 362, F-91405 Orsay Cedex, France Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, People’s Republic of China
热带岛屿生态学教育部重点实验室,海南师范大学生命科学学院,海口571158,中华人民共和国生态系统与进化实验室,CNRS UMR 8079,巴黎南方大学, timent 362, F-91405 Orsay Cedex,法国生物多样性与生态工程教育部重点实验室,北京师范大学生命科学学院,北京100875
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引用次数: 9
Virus evolution in Wolbachia-infected Drosophila. 受狼巴西亚病毒感染果蝇的病毒进化。
Pub Date : 2019-11-06 Epub Date: 2019-10-30 DOI: 10.1098/rspb.2019.2117
Julien Martinez, Gaspar Bruner-Montero, Ramesh Arunkumar, Sophia C L Smith, Jonathan P Day, Ben Longdon, Francis M Jiggins

Wolbachia, a common vertically transmitted symbiont, can protect insects against viral infection and prevent mosquitoes from transmitting viral pathogens. For this reason, Wolbachia-infected mosquitoes are being released to prevent the transmission of dengue and other arboviruses. An important question for the long-term success of these programmes is whether viruses can evolve to escape the antiviral effects of Wolbachia. We have found that Wolbachia altered the outcome of competition between strains of the DCV virus in Drosophila. However, Wolbachia still effectively blocked the virus genotypes that were favoured in the presence of the symbiont. We conclude that Wolbachia did cause an evolutionary response in viruses, but this has little or no impact on the effectiveness of virus blocking.

沃尔巴克氏体是一种常见的垂直传播共生体,可以保护昆虫免受病毒感染,防止蚊子传播病毒病原体。因此,人们正在释放感染了沃尔巴克氏体的蚊子,以防止登革热和其他虫媒病毒的传播。这些计划能否取得长期成功的一个重要问题是,病毒能否进化以逃避沃尔巴克氏体的抗病毒作用。我们发现,狼杆菌改变了果蝇体内 DCV 病毒毒株之间的竞争结果。然而,在有共生体存在的情况下,狼杆菌仍能有效阻止病毒基因型的产生。我们的结论是,沃尔巴克氏体确实引起了病毒的进化反应,但这对病毒阻断的有效性几乎没有影响。
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引用次数: 0
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Proceedings of the Royal Society B
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