Genomic insights into the adaptation and evolution of the nautilus,an ancient but evolving “living fossil”

The nautilus, commonly known as a “living fossil,” is endangered and may be at risk of extinction. The lack of genomic information hinders a thorough understanding of its biology and evolution, which can shed light on the conservation of this endangered species. Here, we report the first high-quality chromosome-level genome assembly of Nautilus pompilius. The assembled genome size comprised 785.15 Mb. Comparative genomic analyses indicated that transposable elements (TEs) and large-scale genome reorganizations may have driven lineage-specific evolution in the cephalopods. Remarkably, evolving conserved genes and recent TE insertion activities were identified in N. pompilius, and we speculate that these findings reflect the strong adaptability and long-term survival of the nautilus. We also identified gene families that are potentially responsible for specific adaptation and evolution events. Our study provides unprecedented insights into the specialized biology and evolution of N. pompilius, and the results serve as an important resource for future conservation genomics of the nautilus and closely related species.     

A history of recent advancements on <Emphasis Type="Italic">Nephrops norvegicus</Emphasis> behavioral and physiological rhythms

Biological rhythms are a widespread feature of living organisms, being expressed at any level of their organization. Behavioral and physiological rhythms can affect the results on species stock assessment when the timing of sampling is not taken into account. That timing is of importance since animals may be present or not in a certain area of sampling depending on their activity cycle. As an example of this, the rhythmic behavior and physiology of one of the most commercially important European decapods, the Norway lobster (Nephrops norvegicus) was studied. These rhythms affect its commercial catchability at a diel and at a seasonal scale. Nephrops inhabits muddy bottoms where animals dig burrows that save them from the trawl tow capture when occupied. Catch patterns have been widely used as proxy of activity rhythms of populations of different depths. Catches show a modulation upon the day-night cycle since animals emerge under optimum environmental illumination in order to feed. Emergence is also affected in a not fully clarified manner by other variables of environmental and demographic nature (e.g. food presence, hunger state, sex, size, reproductive stage, territorialism and mating). All these features make Nephrops a good model of reference for studies on biological rhythms of other commercially important deep water decapods in relation to their ecological context. In this review, we summarize the actual knowledge on Nephrops behavioral and physiological rhythms. We will compare data obtained from laboratory tests on single individuals with data obtained from trawling of populations of different depths. We will also describe some new hypotheses on the rhythmic regulation of the species behaviour, as well as potential scenarios for future research.     

Nanomaterials in the Environment Acquire an “Eco‐Corona” Impacting their Toxicity to Daphnia Magna—a Call for Updating Toxicity Testing Policies

Nanomaterials (NMs) are particles with at least one dimension between 1 and 100 nm and a large surface area to volume ratio, providing them with exceptional qualities that are exploited in a variety of industrial fields. Deposition of NMs into environmental waters during or after use leads to the adsorption of an ecological (eco‐) corona, whereby a layer of natural biomolecules coats the NM changing its stability, identity and ultimately toxicity. The eco‐corona is not currently incorporated into ecotoxicity tests, although it has been shown to alter the interactions of NMs with organisms such as Daphnia magna (D. magna). Here, the literature on environmental biomolecule interactions with NMs is synthesized and a framework for understanding the eco‐corona composition and its role in modulating NMs ecotoxicity is presented, utilizing D. magna as a model. The importance of including biomolecules as part of the current international efforts to update the standard testing protocols for NMs, is highlighted. Facilitating the formation of an eco‐corona prior to NMs ecotoxicity testing will ensure that signaling pathways perturbed by the NMs are real rather than being associated with the damage arising from reactive NM surfaces “acquiring” a corona by pulling biomolecules from the organism's surface.     

Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: A case study using the sea lamprey Petromyzon marinus L.

Many aquatic species of conservation concern exist at low densities and are inherently difficult to detect or monitor using conventional methods. However, the introduction of environmental (e)DNA has recently transformed our ability to detect these species and enables effective deployment of limited conservation resources. Identifying areas for breeding, as well as the ecological distribution of species, is vital to the survival or recovery of a conservation species (i.e., areas of critical habitat). In many species, spawning events are associated with a higher relative abundance of DNA released within an aquatic system (i.e., gametes, skin cells etc.), making this the ideal time to monitor these species using eDNA techniques. This study aims to examine whether a “snapshot” eDNA sampling approach (i.e., samples taken at fixed points in chronological time) could reveal areas of critical habitat including spawning sites for our target species Petromyzon marinus. We utilized a species‐specific qPCR assay to monitor spatial and temporal patterns in eDNA concentration within two river catchments in Ireland over three consecutive years. We found that eDNA concentration increased at the onset of observed spawning activity and patterns of concentration increased from downstream to upstream over time, suggesting dispersal into the higher reaches as the spawning season progressed. We found P. marinus to be present upstream of several potential barriers to migration, sometimes in significant numbers. Our results also show that the addition of a lamprey‐specific fish pass at an “impassable” weir, although assisting in ascent, did not have any significant impact on eDNA concentration upstream after the pass had been installed. eDNA concentration was also found to be significantly correlated with both the number of fish and the number of nests encountered. The application of snapshot sampling techniques for species monitoring therefore has substantial potential for the management of low‐density species in fast‐moving aquatic systems.     

Dynamic digestive responses to increased energy demands in the leaf-eared mouse (<Emphasis Type="Italic">Phyllotis darwini</Emphasis>)

A major area of interest in comparative physiology has been to understand how animals cope with changing environmental demands in time and space. The digestive system has been identified as one of the more sensitive systems to changes in environmental conditions. However, most research on this topic has evaluated these effects during peak energetic demands, which do not allow for evaluation of the dynamics of the digestive response along a more natural continuous gradient of environmental conditions. We examined phenotypic flexibility in digestive responses of the leaf-eared mouse Phyllotis darwini to increments in total energy demands (via sequential exposure to 26, 12 and 0°C). Additionally, we evaluated the effect of a moderate energy demand (12°C) over three different time periods (7, 17 and 27 days) on digestive traits. Moderate increases in energy demand were associated with changes in the distribution of digesta in the gut, whereas higher increases in energy demand involved increases in the tissue mass of digestive organs. Time-course analysis showed that at 12°C practically all digestive variables reached stable values within 7 days, which is in agreement with empirical data and theoretical deductions from cellular turnover rates. We conclude that although the input of energy and nutrients into the digestive tract is typically periodic, many aspects of digestive physiology are likely to be flexible in response to environmental variability over both short-term (daily) and long-term (seasonal) time scales.     

综述: 秀丽线虫胰岛素类生长因子和雷帕霉素受体信号通路对衰老的调节作用

衰老表现为随着时间推移而带来的功能上的衰退和死亡率的上升.利用模式生物,研究人员已经证明,衰老受高度保守的信号通路所调控,而且遗传与环境因素的改变可以显著延长寿命并延缓功能上的衰退.作为一种模式生物,秀丽线虫由于其遗传操作的简单性以及基因组的高度保守性,已被广泛应用于现代生物学研究中.许多关于衰老的分子机理最初是在秀丽线虫中被阐明的.本文总结了秀丽线虫中高度保守的胰岛素类生长因子(IGF-1)和雷帕霉素受体(TOR)这两条信号通路调控衰老的研究进展,并对未来的研究方向展开了评述.     

Conservation In vitro of threatened plants—Progress in the past decade

Summary In vitro techniques have found increasing use in the conservation of threatened plants in recent years and this trend is likely to continue as more species face risk of extinction. The Micropropagation Unit at Royal Botanic Gardens, Kew, UK (RBG Kew) has an extensive collection of in vitro plants including many threatened species from throughout the world. The long history of the unit and the range of plants cultured have enabled considerable expertise to be amassed in identifying the problems and developing experimental strategies for propagation and conservation of threatened plants. While a large body of knowledge is available on the in vitro culture of plants, there are limited publications relating to threatened plant conservation. This review highlights the progress in in vitro culture and conservation of threatened plants in the past decade (1995–2005) and suggests future research directions. Works on non-threatened plants are also included wherever methods have applications in rare plant conservation. Recalcitrant plant materials collected from the wild or ex situ collections are difficult to grow in culture. Different methods of sterilization and other treatments to establish clean material for culture initiation are reviewed. Application of different culture methods for multiplication, and use of unconventional materials for rooting and transplantation are reviewed. As the available plant material for culture initiation is scarce and in many cases associated with inherent problems such as low viability and endogenous contamination, reliable protocols on multiplication, rooting, and storage methods are very important. In this context, photoautotrophic micropropagation has the potential for development as a routine method for the in vitro conservation of endangered plants. Long-term storage of material in culture is challenging and the potential applications of cryopreservation are significant in this area. Future conservation biotechnology research and its applications must be aimed at conserving highly threatened, mainly endemic, plants from conservation hotspots.     

Cellular “bauplans”: Evolving unicellular forms by means of Julia sets and Pickover biomorphs

The universe of cellular forms has received scarce attention by mainstream neo-Darwinian views. The possibility that a fundamental trait of biological order may consist upon, or be guided by, developmental processes not completely amenable to natural selection was more akin to previous epochs of biological thought, i.e. the “bauplan” discussion. Thirty years ago, however, Lynn and Tucker studied the biological mechanisms responsible for defining organelles position inside cells. The fact that differentiated structures performing a specific function within the eukaryotic cell (i.e. mitochondrion, vacuole, or chloroplast) were occupying specific positions in the protoplasm was the observational and experimental support of the ‘morphogenetic field’ notion at the cellular level. In the present paper we study the morphogenetic field evolution yielding from an initial population of undifferentiated cells to diversified unicellular organisms as well as specialized eukaryotic cell types. The cells are represented as Julia sets and Pickover biomorphs, simulating the effect of Darwinian natural selection with a simple genetic algorithm. The morphogenetic field “defines” the locations where cells are differentiated or sub-cellular components (or organelles) become organized. It may be realized by different possibilities, one of them by diffusing chemicals along the Turing model. We found that Pickover cells show a higher diversity of size and form than those populations evolved as Julia sets. Another novelty is the way that cellular organelles and cell nucleus fill in the cell, always in dependence on the previous cell definition as Julia set or Pickover biomorph. Our findings support the existence of specific attractors representing the functional and stable form of a differentiated cell—genuine cellular bauplans. The configuration of the morphogenetic field is “attracted” towards one or another attractor depending on the environmental influences as modeled by a particular fitness function. The model promotes the classical discussions of D’Arcy Thompson and the more recent views of Waddington, Goodwin and others that consider organisms as dynamical systems that evolve through a ‘master plan’ of transformations, amenable to natural selection. Intriguingly, the model also connects with current developments on mechanobiology, highlighting the informational–developmental role that cytoskeletons may play.     

指甲兰属种质资源概况及其研究进展

该文综述了指甲兰属种质资源的历史、地理分布概况和保护现状,以及该属植物在组织培养、药用价值及化学成分分析、香味成分研究与种系发生等领域的国内外研究成果,并对该属植物在未来的研究重点进行了探讨和分析。结果表明:指甲兰属植物是热带地区重要的花卉,具有极高的观赏价值和药用价值,通过有效地保护和利用好该属资源,并在多个学术领域内开展该属植物研究,不仅可以为相关研究提供技术参考和理论支持,而且能够充分挖掘其应用价值。然而,国内外在相关领域的各项研究进展还不够深入,未来指甲兰属植物应加强以下方面的研究:(1)开展资源引种与回归保育等方面的实践工作及研究;(2)利用稀缺资源和母本优势,开展组织培养与属间品种培育方面的研究;(3)充分发掘其药用价值,积极开展植物化学成分方面的研究;(4)开展指甲兰属香味成分分析与应用研究,进而开展该属传粉生物学的研究;(5)利用分子生物学领域的最新技术和方法,揭示出该属在相关类群中的地位和其界定范围。     

Rejoinder to Discussions on “Approval policies for modifications to machine learning‐based software as a medical device: A study of bio‐creep”

We thank the discussants for sharing their unique perspectives on the problem of designing automatic algorithm change protocols (aACPs) for machine learning‐based software as a medical device. Both Pennello et al. and Rose highlighted a number of challenges that arise in real‐world settings, and we whole‐heartedly agree that substantial extensions of our work are needed to understand if and how aACPs can be safely deployed in practice. Our work demonstrated that aACPs that appear to be harmless may allow for biocreep, even when the data distribution is assumed to be representative and stationary over time. While we investigated two solutions that protect against this specific issue, many more statistical and practical challenges remain and we look forward to future research on this topic.     

A synopsis of suggested approaches to address potential competitive interactions between Barred Owls (<Emphasis Type="Italic">Strix varia</Emphasis>) and Spotted Owls (<Emphasis Type="Italic">S. occidentalis</Emphasis>)

The conservation of Spotted Owl (Strix occidentalis) populations has been one of the most controversial and visible issues in United States conservation history. Coincident with declines in Spotted Owl populations over the last three decades has been the invasion of Barred Owls (Strix varia) throughout the range of the Northern Spotted Owl (S. o. caurina) and into the range of the California Spotted Owl (S. o. occidentalis). This invasion has confused the reasons behind recent Spotted Owl declines because anecdotal and correlative information strongly suggests that Barred Owls are a new factor influencing the declines. There is great uncertainty about all aspects of the invasion, and this has sparked discussion about appropriate management and research responses regarding the effects of this invasion on Spotted Owls. We present a set of possible responses to address the issue, and we discuss the relative merits of these with regard to their efficacy given the current state of knowledge. We recommend that research specifically aimed at learning more about the interspecific relationships of these two owls throughout the range of sympatry should begin immediately. Approaches that seem unlikely to be useful in the short-term either because they do not facilitate knowledge acquisition, are relatively costly, or would be technically less feasible, should not be considered viable at this time. We believe the consequences of the invasion are potentially dire for the Spotted Owl and that research and management actions, including the use of adaptive management, are required to inform the near- and long-term decision-making process for conservation of Spotted Owls.     

Genetic diversity of small populations: Not always “doom and gloom”?

Is a key theory of evolutionary and conservation biology—that loss of genetic diversity can be predicted from population size—on shaky ground? In the face of increasing human‐induced species depletion and habitat fragmentation, this question and the study of genetic diversity in small populations are paramount to understanding the limits of species’ responses to environmental change and to providing remedies to endangered species conservation. Few empirical studies have investigated to what degree some small populations might be buffered against losses of genetic diversity. Even fewer studies have experimentally tested the potential underlying mechanisms. The study of Schou, Loeschcke, Bechsgaard, Schlotterer, and Kristensen ( 2017 ) in this issue of Molecular Ecology is elegant in combining classic common garden experimentation with population genomics on an iconic experimental model species (Drosophila melanogaster). The authors reveal a slower rate of loss of genetic diversity in small populations under varying thermal regimes than theoretically expected and hence an unexpected retention of genetic diversity. They are further able to hone in on a plausible mechanism: associative overdominance, wherein homozygosity of deleterious recessive alleles is especially disfavoured in genomic regions of low recombination. These results contribute to a budding literature on the varying mechanisms underlying genetic diversity in small populations and encourage further such research towards the effective management and conservation of fragmented or endangered populations.     

Ecological conditions and the distribution of alpine juniper (<Emphasis Type="Italic">Juniperus communis</Emphasis> subsp. <Emphasis Type="Italic">alpina</Emphasis>) in the Hrubý Jeseník Mts

In the Hruby Jeseník Mts of the Czech Republic, research was carried out from 2001–2005 aimed at completing an up-to-date census of alpine juniper [Juniperus communis subsp. alpine (Smith) Čelakovsky] and an evaluation of the overall health status of the populations, and at investigating the impacts of the main environmental factors on the viability of this species. 13 sites were identified with 283 individuals in total, but the sites differed dramatically in the number of recorded individuals. Comparisons with historical literature sources show that the species has been in decline. The main reasons for this decline include: a lack of suitable sites for colonization connected with a lack of adequate disturbance factors, competition from shading trees, and the presumed high age of the juniper populations combined with zero generative reproduction. More than two thirds of the individuals showed slight damage to their assimilation system. A health status of bad or very bad was determined for 5 % of the alpine juniper individuals. These trees in the Hruby Jeseník Mts are also exposed to pressure from some herbivore insects and mammals. The populations are not yet in a literally critical state, but considering the range of impacts affecting them, it will be necessary to pay significant attention to their conservation strategies. Some recommendations for future management are suggested.     

Lemur Diversity in Madagascar

A basic understanding of the taxonomy, diversity, and distributions of primates is essential for their conservation. This review of the status of the taxonomy of lemurs is based on a 5-d workshop entitled “Primate Taxonomy for the New Millennium,” held at the Disney Institute, Orlando, Florida, in February 2000. The aim is not to present a taxonomic revision, but to review our current understanding of the diversity and current and past ranges of lemurs and indicate where there is controversy, discrepancy, or lack of knowledge. Our goal therefore is to provide a baseline for future taxonomic investigation, as well as a clearer focus for research and conservation priorities. We here focus on the lemurs of Madagascar and recognize 5 families, 15 genera, and 99 species and subspecies. We list 39 species of lemurs described since 2000: 2 dwarf lemurs, Cheirogaleus; 11 mouse lemurs, Microcebus; a giant mouse lemur, Mirza; a bamboo lemur, Hapalemur; 17 sportive lemurs, Lepilemur; and 7 woolly lemurs, Avahi. Taxonomic revisions have resulted in the resurrection of a further 9 taxa. However, the figures do not represent the total diversity of Malagasy lemurs because more new species are being identified via new field studies and accompanying genetic research, and should be described in the near future.     

Climate change effects on behavioral and physiological ecology of predator–prey interactions: Implications for conservation biological control

Habitat management under the auspices of conservation biological control is a widely used approach to foster conditions that ensure a diversity of predator species can persist spatially and temporally within agricultural landscapes in order to control their prey (pest) species. However, an emerging new factor, global climate change, has the potential to disrupt existing conservation biological control programs. Climate change may alter abiotic conditions such as temperature, precipitation, humidity and wind that in turn could alter the life-cycle timing of predator and prey species and the behavioral nature and strength of their interactions. Anticipating how climate change will affect predator and prey communities represents an important research challenge. We present a conceptual framework—the habitat domain concept—that is useful for understanding contingencies in the nature of predator diversity effects on prey based on predator and prey spatial movement in their habitat. We illustrate how this framework can be used to forecast whether biological control by predators will become more effective or become disrupted due to changing climate. We discuss how changes in predator–prey interactions are contingent on the tolerances of predators and prey species to changing abiotic conditions as determined by the degree of local adaptation and phenotypic plasticity exhibited by species populations. We conclude by discussing research approaches that are needed to help adjust conservation biological control management to deal with a climate future.     

An integrated framework to identify wildlife populations under threat from climate change

Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential. We consider intraspecific vulnerability and population‐level responses, an important but often neglected conservation research priority. We demonstrate how this framework can be applied to vertebrates with limited dispersal abilities using empirical data for the bat Plecotus austriacus. We use ecological niche modelling and environmental dissimilarity analysis to locate areas at high risk of exposure to future changes. Combining outlier tests with genotype–environment association analysis, we identify potential climate‐adaptive SNPs in our genomic data set and differences in the frequency of adaptive and neutral variation between populations. We assess landscape connectivity and show that changing environmental suitability may limit the future movement of individuals, thus affecting both the ability of populations to shift their distribution to climatically suitable areas and the probability of evolutionary rescue through the spread of adaptive genetic variation among populations. Therefore, a better understanding of movement ecology and landscape connectivity is needed for predicting population persistence under climate change. Our study highlights the importance of incorporating genomic data to determine sensitivity, adaptive potential and range shift potential, instead of relying solely on exposure to guide species vulnerability assessments and conservation planning.     

Quaternary structure of bovine α-crystallin: influence of temperature

The tertiary and quaternary structure of α-crystallin is still a matter of controversy. We have characterized the native α-crystallin quaternary structure by isolating it at the in vivo temperature and solvent conditions. It can be represented by a distribution of expanded particles with a weight average molar mass of 550 000 g/mol. On decreasing (to 4°C) or increasing (up to 50°C) the temperature, the size distribution increases to larger particles. Only at lower temperatures (4°C), a stable population of particles is obtained with weight average molar mass of 700 000 g/mol. In all conditions, α-crystallin behaves as a very expanded particle with a maximum hydrodynamic volume of 3.15 ml/g. The transitions in quaternary structure are rather slow: it takes several hours to evolve from a population of aggregates, characteristic for given solvent conditions, to another distribution in size and quaternary structure on changing the environment. The quaternary structure of α-crystallin is an uncharacteristic parameter of the particle: a broad distribution of values can be obtained on changing the environment. Any realistic model should include this property. Our studies favor an open loose structure, where peptides can be added or removed without drastic changes of secondary and tertiary structure of the peptides.     

Partnering conservation actions. <Emphasis Type="Italic">Inter situ</Emphasis> solutions to recover threatened species in South West Western Australia

South West Western Australia has a rich endemic flora of global significance. The threats facing this floral diversity are increasing in type, severity and scale, demonstrated by the rising numbers of species threatened with extinction. In particular, the root-rot pathogen Phytophthora cinnamomi is causing widespread destruction, threatening the survival of many of the region’s unique plants. In situ conservation of wild plants is considered the most essential component of a flora conservation program, but the ability to conserve some species adequately is often unachievable in the short term and urgent management intervention is required to prevent extinction. We present data on the status and management of wild populations of four threatened species from the region, including an ex situ program, and describe our efforts to bridge the gap between these two components. Such inter situ conservation recovery work enables monitoring of biological attributes, research into reproductive biology and collection of genetic material for further ex situ conservation, and provides the source of material for future restoration of wild populations.     

Island area,body size and demographic history shape genomic diversity in Darwin's finches and related tanagers

Genomic diversity is the evolutionary foundation for adaptation to environmental change and thus is essential to consider in conservation planning. Island species are ideal for investigating the evolutionary drivers of genomic diversity, in part because of the potential for biological replicates. Here, we use genome data from 180 individuals spread among 27 island populations from 17 avian species to study the effects of island area, body size, demographic history and conservation status on contemporary genomic diversity. Our study expands earlier work on a small number of neutral loci to the entire genome and from a few species to many. We find significant positive correlation between island size and genomic diversity, a significant negative correlation between body size and genomic diversity, and that historical population declines significantly reduced contemporary genomic diversity. Our study shows that island size is the key factor in determining genomic diversity, indicating that habitat conservation is key to maintaining adaptive potential in the face of global environmental change. We found that threatened species generally had a significantly smaller values of Watterson's theta (θ_W = 4N_eμ) compared to nonthreatened species, suggesting that θ_W may be useful as a conservation indicator for at‐risk species. Overall, these findings (a) provide biological insights into how genomic diversity scales with ecological, morphological and demographic factors; and (b) illustrate how population genomic data can be leveraged to better inform conservation efforts.