Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: -19 PreprintsProtocolsVideosJournalsTools & a 10. 21203/rs. 3. rs-4187714/v1This work is licensed under a CC BY 4. 0 LicenseStatus:Under ReviewVersion 1posted 12You are reading this latest preprint versionAbstract(Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of 8 Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and 6 outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of 10 codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. originated in the and diversified in the Late Eocene, and Juglandaceae originated in the and differentiated in Middle Cretaceous.

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: We considered that the variance in ɛp* is approximately the sum of the true variance in relative paternity shares plus the sire variance in relative juvenile survival (up to the time of sampling). Assuming additive genetic effects, this sire variance is at best equal to half of the variance in survival among full-sib families (i. e. , clutches sired by a single father). We therefore computed the latter and compared it to the variance in ɛp* to get an idea of the maximum fraction of our postcopulatory component that is due to sire effects on juvenile survival. 480 possible copulations (as copulation is unilateral in P. acuta, there are two possibilities for each of the 240 possible pairs of individuals), 255 were actually observed, 119 of which were observed repeatedly (combinations that were repeated two, three, and four times were observed in 98, 15, and six cases, respectively). Offspring from 104 broods survived to genotyping age (8529 juveniles of 10,070 eggs), and 120 adults and 2188 juveniles were genotyped. Four snails copulated as females with two partners but laid no eggs, and six individuals never copulated as females and laid no eggs either. No selfing was detected. None of the 24 broods with a single behavioral father (i. e. , an individual that has been seen inseminating the focal) had more than a single genetic father, indicating that we probably detected all copulations. The remaining 86 individuals copulated as females with at least two male partners and laid eggs that produced 5854 surviving juveniles. Multiple paternity was actually detected in 67. 4% of these broods (58 of 86), with up to three fathers per brood. were characterized by their duration, male experience, sperm age, and male rank. Only rank turned out to significantly influence siring success (Table 1). The first copulation yielded the strongest fitness benefit to males, each subsequent copulation yielding on average 1. 42 times less siring success than the previous one (Fig. 2). Adding the contribution of subsequent copulations (after the first one) increased the predicted number of sired offspring by only a small amount, meaning that subsequent copulations contribute relatively little to siring success (Fig. 2).

Output: corroborate


Input: Claim: Fungi can only grow in damp and dark environments and cannot survive in dry areas. [SEP] Text: defined better his thought saying: “Proponents of contraction want to create integrated, self-sufficient and materially responsible societies in both the North and the South. It might be more accurate and less alarming if we replaced the word degrowth with ‘nongrowth’. We could then start talking about ‘a-growthism’, as in ‘a-theism’. After all, rejecting the current economic orthodoxy means abandoning a faith system, a religion. To achieve this, we need doggedly and rigorously to deconstruct the matter of development. The term ‘development’ has been redefined and qualified so much that it has become meaningless” (Latouche, 2004). In addition, he strongly criticized the “no-global movement” because members are well aware about harms related to economic growth but they are fighting in order to enable developing countries to benefit from it. 3. Sustainable development is a mainstream of environmentalism that, like the de-growth theory, highlights the necessity to stem environmental exploitation and the necessity to improve efficiency of the industrial system in order to limit waste of important natural resources. Nevertheless, this mainstream is not trying to limit economic growth, because the key word in this case is “efficiency”. De-growth theory describes Capitalism as an enemy, to the opposite, roots of are inside Capitalism. Joseph Schumpeter, an economist and political scientist, was one of the progenitors of the 20th century Capitalism. He developed a theory very focused on efficiency: according to Schumpeter, Capitalism is able to ensure, automatically, the predominance of effective enterprises at the expense of inadequate enterprises. He defined this theory “Creative Destruction” writing that is “the essential fact about capitalism. It is what capitalism consists in and what every capitalist concern has got to live in” (Schumpeter, 1976). This theory has become an important part of the theoretical structure of Sustainable Development. In a world where natural resources are every day more limited, efficiency is very related to the capacity of improve the productivity while using less resources. This is an important point because it turns upside down the line of reasoning of Degrowth theory: enterprises have to become more efficient in order not only to survive but also to increase profits. In terms of productivity, it would mean increasing the markup per single resource utilized: that is not only economy but also philosophy.

Output: pass


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: The phylogeny and divergence times didn’t support rapid radiation occurred in the evolution history of Engelhardia. study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family. EngelhardiaplastomesPhylogenetic relationshipsInsertion and deletionCodon usage patternFiguresFigure 1Figure 2Figure 3Figure 4Figure 5Figure 6Figure 7Figure 8Figure 9IntroductionThe walnut family (Juglandaceae) containing ca. 60 extant species belonging to ca. 10 genera, a woody family in the order Fagales, is mainly distributed in subtropical to tropical forests [1] [2] [3]. Members of this family play an important role in local forest ecosystems, and some of them are important nut, timber, and medicinal trees. According to APG IV (2016), Juglandaceae is grouped into three subfamilies: Rhoipteleoideae, Engelhardioideae, and Juglandoideae [4]. Among the three subfamilies of Juglandaceae, species of the Juglandoideae subfamily were very common in temperate deciduous forests in the Northern Hemisphere, while species of the Engelhardioideae subfamily and the Rhoipteleoideae subfamily were mainly distributed in subtropical and tropical forests [2]. In the Engelhardioideae subfamily, species of Engelhardia Lesch. ex Blume widely distributed in the tropical and subtropical regions of eastern Asia [5], which were widely used in wood and tea [6]. There are about 9 Engelhardia species in China, mainly occuring in the southwest, south to southeast [7]. species are deciduous or semi-evergreen trees or evergreen tree, often with even-pinnate compound leaves, monoecious or dioecious, fruit nut-like, when the fruit is ripe, the bracts grow, membranous, and connate with the fruit to form a nutlet with 3-lobed wings [8].

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: Early copulations yielded more paternities than late ones and the second, third, and fourth copulations made by a male-acting individual on a single female contributed weakly to siring success (Fig. 2). This strongly suggests that selection in P. acuta favors individuals that are efficient at finding (and copulating with) potential female mates before competitors. Longer copulations did not result in more efficient fertilization of female-acting partners, suggesting that they were not associated with the injection of more sperm or accessory substances, as found in other species (Koene and Schulenburg 2005; Eberhard 2009). That male experience had no effect suggests that male-acting individuals were not sperm limited. In addition, at the time scale of our experiment (a few days), sperm fertilization success was not affected by its residence time in female reproductive tracts, which is not surprising given the ability of most freshwater snails (including P. acuta) to store sperm for several weeks (Jarne et al. 2010). First-male sperm precedence is not uncommon, especially in snails (e. g. , Rogers and Chase 2002; Evanno et al. 2005; Harano et al. 2008), although many animal species tend to show last-male precedence, including some insects (e. g. , Pischedda and Rice 2012) and hermaphroditic invertebrates (e. g. , Angeloni et al. 2003; Pongratz and Michiels 2003). However, in the majority of studies investigating the distribution of paternity shares in mating groups, the quantitative estimates of siring success are likely biased (Schärer 2009), because they usually erase substantial variation in the copulatory sequence, either by inferring copulations from genetic data rather than from behavioral observations (e. g. , Pongratz and Michiels 2003; Pischedda and Rice 2012), or by using sequential designs preventing competition for access to mates (e. g. , Rogers and Chase 2002; Evanno et al. 2005; Harano et al. 2008). A central aspect of our work is the decomposition of variance in fitness into several components, an approach first proposed by Arnold and Wade (1984a,b) and already used in previous studies (Collet et al. 2012; Pischedda and Rice 2012). Our method differs from Arnold and Wade's in two important ways.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: Mushrooms and Fungi and Compounds with Antidiabetic Activity: A Review Issue 5, 2024, 10. 1615/IntJMedMushrooms. 2024052864 Submitted: Feb 15 2024 Accepted: Feb 15 2024 Published online: Feb 16 2024 Get access Maura Téllez-Téllez Laboratory of of Morelos State, Morelos, Mexico Díaz-Godínez Gerardo (Corresponding author gerardo. diaz@uatx. mx) for Biological Sciences, of have been used by humans for centuries as food and medicine because they have been shown to affect certain diseases. Mushrooms for medicinal purposes have been consumed in the form of extracts and/or biomass of the mycelium or fruiting body. The beneficial health effects of mushrooms are due to their content of bioactive compounds (polysaccharides, proteins, ergosterol, lectins, etc. ). On the other hand, diabetes is one of the metabolic diseases that affects the population worldwide, characterized by hyperglycemia that involves a defective metabolism of insulin, a hormone secreted by β cells and that mainly stimulates glucose absorption by the cells. However, it also affects the metabolism of carbohydrates, fats and proteins; poor control of this disease leads to serious damage to eyesight, kidneys, bones, heart, skin, blood vessels, nerves, etc. It has been reported that the consumption of some mushrooms helps control and treat diabetes, since among other actions, they promote the secretion of insulin by the pancreas, help reduce blood glucose and have α-glucosidase inhibitory activity which improves glucose uptake by cells, which are effects that prescription medications have for patients with diabetes. In that sense, this manuscript shows a review of scientific studies that support the abilities of some mushrooms to be used in the control and/or treatment of diabetes. : Ascomycetes, Basidiomycetes, diabetes mellitus, mycopharmaceuticals, medicinal mushrooms and fungi 9291. Organization. Diabetes (cited 2023 Sept 21). Available from: Organization. Traditional, complementary and integrative medicine [cited 2023 Sept 21]. Available from: Hobbs C. Medicinal mushroom: An exploration of tradition, healing and culture. Summertown, TN: Botanica Press; 2002. Wasser SP.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: In previous studies on the species delimitation of Engelhardia [7] [9] and the phylogeography of two trees species (i. e. , E. roxburghiana and E. fenzelii) [10], combined plastid regions (psbA-trnH, trnL-trnF, rps16, trnS-trnG, and rpl32-trnL), one nuclear ribosomal internal transcribed spacer (nrITS), and Microsatellite (nSSR) data were used. Yet to date, except in individual cases [3] [11] [12], comparative analyses of multiple Engelhardia plastome are still lacking. Plastomes, as critical organelles, play a pivotal role in plant cells, underscored by their widespread application in evolutionary and phylogenetic studies [13, 14]. Their importance is attributed to maternal uniparental inheritance and a highly conserved structure, making them valuable in dissecting plant evolutionary histories and relationships across a wide array of studies [15, 16]. Plastome is usually a closed circular tetrad structure composed of DNA double-stranded molecules, including a large single copy region (LSC), a small single copy region (SSC) and a pair of inverted repeat region (IRa/IRb) [17]. Early phylogenetic analyses used partial plastomes DNA sequences. However these fragments did not have enough information to distinguish closely related plant species, while whole plastid genomes can provide in-depth information to improve our understanding of species evolution [18]. The complete plastomes had made great progress in elucidating the relationship in monocot [19], and also explained the relationship between several major lineages of angiosperms [20]. Meanwhile, plant plastome gene and genome evolving during the process of speciation can help us understand how species adapts to diverse ecological habitats [14]. In the study of phylogeny and evolution of species, fossils play a crucial role in determining the time of species differentiation [21]. For example, the well preserved fossils were helpful to provide insights into the life cycle of early land plants [22], and the usage of fossil correction and molecular clock methods can well support the pre-Cretaceous origin of angiosperms [23].

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: Sign in through your institution Filter EvolutionThis issue Biological SciencesEvolutionary BiologyScience and search term Advance 10. 1111/evo. 12994 Published: 01 September 2016 10. 1111/evo. 12994 Select format. ris (Mendeley, Papers, Zotero). enw (EndNote). bibtex (BibTex). txt (Medlars, RefWorks) Download citation issue Biological SciencesEvolutionary BiologyScience and search term issue Biological SciencesEvolutionary BiologyScience and search term speciation occurs when reproductive isolation evolves between populations adapting to contrasting environments. A key prediction of this process is that the fitness of hybrids between divergent populations should be reduced in each parental environment as a function of the proportion of local genes they carry, a process resulting in ecologically dependent reproductive isolation (RI). To test this prediction, we use reciprocal transplant experiments between adjacent populations of an Australian wildflower, Senecio lautus, at two locations to distinguish between ecologically dependent and intrinsic genetic reproductive barriers. These barriers can be distinguished by observing the relative fitness of reciprocal backcross hybrids, as they differ in the contribution of genes from either parent while controlling for any intrinsic fitness effects of hybridization. We show ecologically dependent fitness effects in establishment and survival of backcrosses in one transplant experiment, and growth performance in the second transplant experiment. These results suggest natural selection can create strong reproductive barriers that maintain differentiation between populations with the potential to interbreed, and implies a significant role for ecology in the evolutionary divergence of S. lautus. Ecological speciation, MCMCglmm, postzygotic isolation, reciprocal transplant, SenecioSpeciation is the process whereby populations become reproductively isolated from one another (Coyne and Orr 2004). Understanding the drivers of this process requires examination of the factors that prevent gene exchange between populations and their relative contributions to reproductive isolation (Sobel et al. 2010). Barriers to gene flow fall into two main categories: those that prevent mating between populations and therefore prevent the formation of hybrids (prezygotic), and those that prevent hybrids from mating if they are produced (postzygotic).

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: Medicinal mushrooms as a source of antitumor and immunomodulating polysaccharides. Biotechnol. 2002;60:258-74. Worthington J, Rashid S. The therapeutic potential of mushroom extracts. In: Natural products as future medicinal agents. Philadelphia: Publishing; 2009. p. 49-72. . Ethnomycological study in the Kilum-Ijim mountain forest, Northwest Region, Cameroon. J Ethnobiol Ethnomed. 2018;14:25. Smith JE, Sulivan R. approach to medicinal mushrooms. Technol. 2004;4:145-55. . Effect of medicinal mushrooms on blood cells under conditions of diabetes mellitus. Diabetes. 2017;8:187-201. . S. Antidiabetic activity of Taxus cuspidata polysaccharides in streptozotocin-induced diabetic mice. Biol Macromol. 2012;50:720-4. . Protective effect of selenium-polysaccharides from the mycelia of Coprinus comatus on alloxan-induced oxidative stress in mice. Food Chem. 2009;117:42-7. . Recent advances in pharmacotherapy for hypertriglyceridemia. J Lipid Res. 2014;56:47-66. . Antidiabetic effect of polysaccharides from Pleurotus ostreatus in streptozotocin-induced diabetic rats. Biol Macromol. 2016;83:126-32. -Hwang L, Wang PS. Inhibitory mechanisms of Agaricus blazei Murrill on the growth of prostate cancer in vitro and in vivo. J Nutr Biochem. 2009;20:753-64. . Increased gene expression of antioxidant enzymes in KKAy diabetic mice but not in STZ diabetic mice. Clin Pract. 2005;69:113-9. . Medicinal mushrooms for glycemic control in diabetes mellitus: History, current status, future perspectives, and unsolved problems (review). Med Mushr. 2011;13:401-26. . Medicinal mushrooms in prevention and control of diabetes mellitus. Fungal Divers. 2012;56:1-29. .

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Previous studies based on fossil evidence have greatly promoted our understanding of Juglandaceae as a whole [2, 24], but for subfamily Engelhardioideae, generally only showing the differentiation time of E. roxburghiana due to insufficient sampling. Therefore, the divergence times of the Engelhardioideae species remain unsolved. In this study, a total of 14 individuals from eight species of Engelhardia (E. anminiana, E. fenzlii, E. hainanensis, E. roxburghiana, E. serrata, E. spicata, E. spicata var. rigida, and E. villosa) and one outgroup species Rhoiptelea chiliantha were newly sequenced (Table 1), and 42 plastome sequences from 36 Juglandaceae species and 6 outgroup species were downloaded from GenBank. The whole plastomes were used to explore evolution and the deep phylogenetic relationship among the species of Engelhardia and (or) other genera, subfamilies, even the whole Juglandaceae family. Our specific goals were as follows: (1) to compare the plastomes and identify the variation in Engelhardia; (2) to identify genomic structural variation across Juglandaceae plastomes; (3) to deepen the understanding on the codon usage bias and gene evolution in Juglandaceae plastomes; (4) to infer and test the phylogenetic relationship and divergence time among the genera and subfamilies of Juglandaceae using plastome data. Table 1 Taxa, voucher and GenBank accession numbers of Engelhardia species and Rhoiptelea chiliantha sequenced in this study. Species DNA code Voucher no.

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: These barriers may be independent of the environment in which they are measured (intrinsic) and arise from the evolution of genetic incompatibilities between populations (Orr and Turelli 2001), or act only in the local habitats of the diverging populations (extrinsic) and result from adaptation via divergent natural selection arising from ecological differences between populations (Schluter 2001). While intrinsic genetic isolating barriers may evolve in both ecological and nonecological modes of speciation, the presence of extrinsic postzygotic isolation, especially where intrinsic barriers are low, provides strong support for ecological speciation (Hatfield and Schluter 1999; Seehausen et al. 2014). If extrinsic postzygotic isolation is present between diverging populations, it follows that intrinsic postzygotic barriers must be weak enough to produce viable hybrids in the laboratory, but ecological differences between populations create sufficient pressure on hybrids that they suffer fitness reductions under field conditions (Rundle and Whitlock 2001). This prediction arises because of two reasons: first, hybrid genotypes lack the adaptive phenotypes under selection in the habitat of each diverging population and therefore have reduced fitness relative to their parents (Nosil et al. 2005; Sobel et al. 2010); and second, reduction in hybrid fitness in parental but not in laboratory environments arises from adaptation to contrasting environments (Hatfield and Schluter 1999), and not from genetic-based incompatibilities that reduce fitness under stressful conditions (Rundle and Whitlock 2001; Coyne and Orr 2004). Not surprisingly, separating hybrid fitness reductions arising solely from ecologically based divergent natural selection from those resulting from the evolution of intrinsic genetic incompatibilities between taxa remains a challenging exercise (Rice and Hostert 1993; Dettman et al. 2007; Egan and Funk 2009; McBride and Singer 2010). Moreover, early generation hybrids often show patterns of heterosis that may obscure the fitness effects of ecologically based selection (Lowry et al. 2008; Baack et al. 2016), further complicating the contributions of extrinsic postzygotic isolation to speciation. In response to these difficulties, Rundle and Whitlock (2001) proposed an elegant approach to demonstrate the effects of ecological divergent natural selection on the evolution of reproductive isolation during speciation.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: Hypoglycemic activity of the fungi Cordyceps militaris, Cordyceps sinensis, Tricholoma mongolicum, and Omphalia lapidescens in streptozotocin-induced diabetic rats. Biotechnol. 2006;72:1152-6. Lu YJ, Wu J. Therapeutic effect of jinshuibao capsules combined with alprostadil injection in treatment of diabetic nephropathy: A report of 30 cases. Med. 2013;12:86-7. . Chemical composition of five wild edible mushrooms collected from and their antihyperglycemic and antioxidant activity. Toxicol. 2012;50:1238-44. . Antihyperglycemic, antihyperlipidemic and antioxidant activities of polysaccharides from Catathelasma ventricosum in streptozotocin-induced diabetic mice. Toxicol. 2013;57:39-45. . Structural characterization and antidiabetic activity of a glucopyranose-rich heteropolysaccharide from Catathelasma ventricosum. Carbohydr Polym. 2016;149:399-407. . Antioxidation, anti-hyperglycaemia and renoprotective effects of extracellular polysaccharides from Pleurotus eryngii SI-04. Biol Macromol. 2018;111:219-28. . Glucan-rich polysaccharides from Pleurotus sajor-caju (Fr. ) Singer prevents glucose intolerance, insulin resistance and inflammation in C57BL/6J mice fed a high-fat diet. . 2012;12:261. -Towatana N, Wititsuwannakul R. (Beta)-glucan-containing polysaccharide extract from the grey oyster mushroom (Pleurotus sajor-caju (Fr. ) Sing. ) stimulates glucose uptake by the L6 myotubes. Res J. 2014;21:779-84. . Evaluation of antidiabetic activity of polysaccharide isolated from Phellinus linteus in non-obese diabetic mouse. Intern Immunopharmacol. 2010;10:72-8. FC, de.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: anminiana MHH2018001-02 Hong-OR208248 Sulawesi province, fenzelii JNSX01 ZYH19072801 Yong-OP480035 01 ZYH17102801 Yong-OP480037 Tiantangding, Guangzhou, Guangdong, hainanensis 02 MHH20170514001A Hong-OR208247 01 ZYH18072101 Yong-OP480038 Jianfengling, Ledong, Hainan, roxburghiana BPZ11 ZYH17120911 Yong-OP480042 02 ZYH18072103 Yong-OP480031 06 ZYH17121606 Yong-OP480033 01 ZYH19011503 Yong-OP480034 serrata MHH201800103-10 Hong-OR208250 Sulawesi province, spicata MHH2018092101-01 Hong-OR208253 spicata var. rigida MHH20180922015-16 Hong-OR208251 Sumatra Island, villosa MHH2018032813-20 Hong-OR208252 Niukong, Lvchun, Yunnan, chiliantha MWS2 LP174627 OP480039 of Engelhardia plastomes The lengths of the complete plastomes of Engelhardia were slightly different, ranging from 161,069 bp to 162,336 bp, exhibiting a quadripartite structure with a large singlecopy (LSC) region (89,927–91,637 bp), dual inverted repeat (IR) regions (25,813–26,016 bp), and a small single-copy (SSC) region (18,790–19,203 bp) (Fig. 1; Table 2). There were a total of 134 genes were identified in the newly sequenced plastomes, including 88 protein-coding genes (CDS), 2 pseudogenes (Ψycf1、Ψrps19), 37 transfer RNA (tRNA) genes and 8 ribosomal (rRNA) genes (Table 2).

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: Headland and Dune pairs appear to have evolved repeatedly and independently on multiple occasions (Roda et al. 2013a,b), a pattern that is consistent with parallel adaptation to similar ecological conditions. In the populations used in this experiment, estimates of genetic divergence are low (Fst = 0. 08 for Coffs Harbour, and Fst = 0. 09 for population; Roda et al. 2013a), which suggests recent divergence or gene flow between populations. However, a small fraction of the genome shows fixed genetic differences indicating that population boundaries are possibly maintained by divergent natural selection (Roda et al. 2013a). Previous work also discovered that local adaptation to coastal environments creates strong immigrant inviability between S. lautus ecotypes (Melo et al. 2014; Richards and Ortiz-Barrientos 2016). While ecotypes are genetically differentiated and occur in contrasting ecological conditions, intrinsic barriers to gene flow are weak, (Richards and Ortiz-Barrientos 2016), and populations still retain the ability to produce viable hybrid crosses when grown in a common environment (Ali 1966; Melo et al. 2014; Richards and Ortiz-Barrientos 2016). These characteristics provide an ideal opportunity to investigate the specific contributions of ecological divergent natural selection to the evolution of postzygotic reproductive isolation and thus to examine the role of ecological speciation in the origin of new plant species. Here, we present results from two field-based reciprocal transplant experiments designed to test for the presence of ecological reproductive isolation between coastal populations of S. lautus. We include parental as well as F1 and F2 hybrids, and backcrosses between the Dune and Headland ecotypes at Lennox Head, and between Dune, Headland and Island ecotypes of S. lautus at Coffs Harbour. We ask whether ecological divergent natural selection can produce barriers to gene flow between these coastal ecotypes, as predicted by the ecological speciation hypothesis. We discuss how these results help us better understand how natural selection may drive speciation when there is opportunity for gene flow, and the similarities of the origin of species across the natural kingdoms. Materials and seeds used in these experiments were derived from seed collected in natural populations at Boambee beach (S 30° 18′ 45. 28″, E 153° 8′ 21. 43″, Dune type), Corambirra point (S 30° 18′ 44.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: Effect of Agaricus blazei Murrill on the pulmonary tissue of animals with streptozotocininduced diabetes. Res 2010;2010:543926. . Phytochemical characteristics and hypoglycaemic activity of fraction from mushroom Inonotus obliquus. J Agr. 2010;90:276-80. . Extract of chaga mushroom (Inonotus obliquus) stimulates 3t3-l1 adipocyte differentiation. Phytother Res. 2010;24:1592-9. ’Souza JJ. Aldose reductase inhibitors in the treatment of diabetic peripheral neuropathy: A review. J Diabetes Compl. 2010;24:354-60. Combs AP. Recent advances in the discovery of competitive protein tyrosine phosphatase 1B inhibitors for the treatment of diabetes, obesity and cancer. J Med Chem. 2010;53:2333-44. . A protein tyrosine phosphatase 1B activity inhibitor from the fruiting bodies of Ganoderma lucidum (Fr. ) Karst and its hypoglycemic potency on streptozotocin-induced type 2 diabetic mice. J Chem. 2011;59:6492-500. . Antidiabetic, antihyperlipidemic and antioxidant activities of a novel proteoglycan from Ganoderma lucidum fruiting bodies on db/db mice and the possible mechanism. PLoS One. 2013;8:e68332. Goulet O. Potential role of the intestinal microbiota in programming health and disease. Nutr Rev. 2015;73:32-40. . Intake of Ganoderma lucidum polysaccharides reverses the disturbed gut microbiota and metabolism in type 2 diabetic rats. Biol Macromol. 2020;155: 890-902. Brem H, Tomic-Canic M. Cellular and molecular basis of wound healing in diabetes. J Clin Invest. 2007;117:1219-22. Giacco F, Brownlee M. Oxidative stress and diabetic complications. Circ Res. 2010;107:1058-70. . Ganoderma lucidum polysaccharide accelerates refractory wound healing by inhibition of mitochondrial oxidative stress in type 1 diabetes. Biochem. 2012;29:583-94. .

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: The ycf1 in the IRb region (Ψycf1) and the rps19 in IRa region (Ψrps19) of all Engelhardia species were identified as pseudogenes (Table S2). Among these genes, there were 18 intron-containing genes, of which three genes rps12, clpP and ycf3, had two introns, and the rest contained a single intron (trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA, trnV-UAC, rpl2, rpl16, rps16, rpoC1, atpF, ndhA, ndhB, petB, and petD) (Table S2). These newly-generated Engelhardia plastomes were deposited in GenBank (showed in Table 1). Table 2 Complete features of 13 newly assembled Engelhardia plastomes and one Rhoiptelea chiliantha plastome. (bp) LSC (bp) SSC (bp) IR (bp) CDS (bp) Total GC content (%) Total genes CDS Pseudo tRNA genes rRNA genes E. Arminian 162,088 91,302 19,054 25,866 78,969 35. 9 134 88 2 37 8 E. fenzelii_JNSX01 161,069 89,927 19,112 26,015 78,867 36. 0 134 88 2 37 8 E. fenzelii_TTD01 161,105 89,964 19,111 26,015 78,867 36. 0 134 88 2 37 8 E. hainanensis_02 161,574 91,157 18,791 25,813 79,137 35. 8 134 88 2 37 8 E. hainanensis_HN01 161,572 91,156 18,790 25,813 79,137 35. 8 134 88 2 37 8 E. roxburghiana_BPZ11 161,713 90,478 19,203 26,016 78,906 35. 9 134 88 2 37 8 E. roxburghiana_JFL02 161,511 90,373 19,106 26,016 78,915 35. 9 134 88 2 37 8 E.

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: determine fitness differences between the parental and hybrid populations, we defined three components of fitness: establishment, survival, and growth performance. While related, these three different measures of fitness allow distinctions to be made across multiple life-history stages, and therefore elucidate whether selection acts in a uniform way across the lifespan of a plant, or whether there are particular developmental stages at which ecological factors have greatest effects on fitness. While flowering and seed production is the best estimate of lifetime fitness, we were unable to get reliable estimates of these traits due to low sample size of flowering plants across the experiment. As mentioned, no plants flowered in the Dune environment. Across the two environments where we have data on flowering, there was a very strong correlation between growth and flower count (r = 0. 78). We therefore used harvest mass in these analyses, as this measure increases sample sizes and provides a reasonable proxy of flower production. We outline the methods for the three fitness components in chronological order from seedling emergence to harvest. Probability of establishment To calculate the fitness of cross types in the field we used a conditional generalized linear-mixed model in a Bayesian framework to estimate the mean probability of germination and establishment for each genotype. These models estimate the probability of an event based on known conditions that may be related to the event. In this case, we estimate the probability of each genotype passing through the initial establishment life-history stage using information about germination. This process takes into account that missing values of later life-history fitness components, such as leaf production, are not missing at random, but may result from systematic patterns in early life-history stages such as germination (Steinsland et al. 2014). We modeled fitness over life-history stages using the conditional response variable (Emergence –> Survival to day 100 –> Ability to produce 10 leaves) for Lennox Head, and (Germination –> Ability to produce seven leaves) for Coffs Harbour, where the arrow (–>) represents the direction of conditionality between each transition. The differences in the models between environments reflect different logistical issues between the two experiments (e. g. , different frequency of data monitoring among transplant sites), but the measures of seven and 10 leaves are equivalent of life-history transition in each population. Analyses were conducted using the R package MCMCglmm (Hadfield 2010).

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: Effects of medicinal mushroom (Sparassis crispa) on wound healing in streptozotocin-induced diabetic rats. Surg. 2009;197:503-9. . Polysaccharides of mushroom Phallus impudicus mycelium: Immunomodulating and wound healing properties. Sci Technol. 2019;35:30-7. . Pancreas protective effect of button mushroom Agaricus bisporus (JE Lange) Imbach (Agaricomycetidae) extract on rats with streptozotocin-induced diabetes. Med Mushrooms. 2010;12;379-89. . White button mushroom (Agaricus bisporus) lowers blood glucose and cholesterol levels in diabetic and hypercholesterolemic rats. Nutr Res. 2010;30:49-56. . Anti-diabetic activity of B-glucans and their enzymatically hydrolyzed oligosaccharides from Agaricus blazei. Biotechnol Lett. 2005;27:483-7. . Semipurified fractions from the submerged-culture broth of Agaricus blazei Murrill reduce blood glucose levels in streptozotocin-induced diabetic rats. J Chem. 2010;58:4113-9. . Isolation and identification of potent antidiabetic compounds from Antrodia cinnamomea-An edible Taiwanese mushroom. Molecules. 2018;23:2864. . Amelioration of streptozotocin-induced diabetes by Agrocybe chaxingu polysaccharide. Mol Cells. 2010;29:349-54. . Role of mushrooms in gestational diabetes mellitus. . 2019;6:49-66. . Hypoglycemic effect of water-soluble polysaccharide from Auricularia auricula-judae Quel. on genetically diabetic KK-Ay mice. Biochem. 1998;62:1898-903. . The effect of boletus polysaccharides on diabetic hepatopathy in rats. Interact. 2019;308:61-9. . Molecular identification, in vivo and in vitro activities of Calvatia gigantea (macro-fungus) as an antidiabetic agent. Mycology. 2019;10:166-73. .

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: roxburghiana_TPS06 161,713 90,478 19,203 26,016 78,906 35. 9 134 88 2 37 8 E. roxburghiana_XSBN01 161,667 90,448 19,187 26,016 78,906 35. 9 134 88 2 37 8 E. serrata 162,161 91,313 19,092 25,878 78,852 35. 9 134 88 2 37 8 E. spicata 161,551 90,937 18,890 25,862 79,113 35. 8 134 88 2 37 8 E. spicata var. rigida 161,520 90,951 18,871 25,849 79,122 35. 9 134 88 2 37 8 E. villosa 162,336 91,637 19,043 25,828 79,143 35. 8 134 88 2 37 8 R. chiliantha_MWS2 161,702 90,447 19,081 26,087 79,182 36. 1 133 88 1 37 8 The overall GC content of Engelhardia plastomes was 35. 8%-36. 0% (Table S3), and the GC contents of coding sequence (CDS) regions was 37. 2%-37. 3%. We found that the GC content of LSC (33. 2–33. 6%) and SSC (29. 3–29. 6%) region were lower than those of IR regions (42. 6–42. 7%) (Table S3). Comparative analysis of Engelhardia plastomes Multiple plastomes comparison among all the Engelhardia species using mVISTA and Mauve alignment showed high degree of collinearity. It was found that the composition and sequence of genes in Engelhardia were highly consistent, and no inversion or translocation of DNA fragment rearrangement was detected in the sequences, which is consistent with the rarity of recombination in plant plastomes [25] (Fig. S2).

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: The local parental population from each habitat had the lowest risk of death, while the immigrant parent had over two times higher risk of dying in that environment (Table S2). Furthermore, in both environments, risk increased with the proportion of foreign genes in the genotype, except for the F1DH genotype in the Dune habitat, which was not significantly different to the Dune parent (relative risk = 0. 88, z = –0. 77, P = 0. 44, Table S2). between Headland and Island, and Dune and Headland populations showed a pattern of ecologically dependent fitness in backcross genotypes (Fig. 4). The significant backcross type-environment interaction term between Headland-Isle (F1,27 = 14. 24, P = 0. 001) and Headland-Dune (F1,3 = 11. 04, P = 0. 045) showed a switch in the fitness rank of reciprocal backcrosses between environments. There was no significant interaction effect between backcrosses between Dune and Island genotypes (F1,21 = 0. 36, P = 0. 556) (Table 1). Figure 4. Comparison of growth performance between recombinant hybrids and parental populations from Coffs Harbour. Harvest mass is log(n + 1) transformed and describes the total biomass accumulation over the lifespan of all surviving plants. and B show the reciprocal transplant between Headland and Island derived populations in each Headland and Island sites. and D describe the Dune-Headland comparison and and F describe Dune-Island comparison, respectively. Dotted lines show significant interactions between backcross type and environment, meaning the mass accumulation was highest in the backcross to the local population that is a diagnostic pattern associated with ecologically dependent reproductive isolation. Open in new tabDownload slide Table 1. Open in new tab Anova of Harvest mass of Backcross genotypes organized by population comparisons valuePr(>F)D-IPopulation11. 5721. 5721. 9590. 176Environment13. 5433. 5434. 4150. 048Block10. 1560. 1560. 1950. 664pop:env10. 2880. 2880. 3580. 556Residuals2116. 8510. 802H-IPopulation10. 8080. 8081. 8540. 185Environment11. 8131. 8134. 1610.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: Hypoglycemic effect of crude exopolysaccharides produced by Cerrena unicolor, Coprinus comatus, and Lenzites betulina isolates in streptozotocin-induced diabetic rats. Pharm Biol. 2009;47:168-74. . Hypoglycemic effects of Ganoderma applanatum and Collybia confluens exo-polymers in streptozotocin-induced diabetic rats. Phytother Res. 2007;21:1066-9. . Hypoglycemic effect of Cordyceps militaris. Pharmacogn. 2001;32:327-9. . Anti-diabetic effects of and cordycepin from Cordyceps militaris and the immune responses in streptozotocin-induced diabetic mice. Sci. 2003;9:291-8. . Improvement of insulin resistance and insulin secretion by water extracts of Cordyceps militaris, Phellinus linteus, and Paecilomyces tenuipes in 90% pancreatectomized rats. Biochem. 2004;68:2257-64. . Hypoglycemic activity of a polysaccharide (CS-F30) from the cultural mycelium of Cordyceps sinensis and its effect on glucose metabolism in mouse liver. Phytother Res. 2000;4:647-9. . Hypoglycaemic effect of comatin, an antidiabetic substance separated from Coprinus comatus broth, on alloxan-induced-diabetic rats. Food Chem. 2010;121:39-43. . Effects of aqueous extract of Ganoderma lucidum on blood glucose levels of normoglycemic and alloxan-induced diabetic Wistar rats. J Res. 2007;1:34-7. . Anti-diabetic effects of Ganoderma lucidum. Phytochemistry. 2015;114:109-13. . Antidiabetic activity of Ganoderma lucidum polysaccharides F31 down-regulated hepatic glucose regulatory enzymes in diabetic mice. J Ethnopharmacol. 2017;196:47-57. . Triterpenes and meroterpenes from Ganoderma lucidum with inhibitory activity against HMGs reductase, aldose reductase and a-glucosidase. Fitoterapia.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: The regions with relatively low identity were rps16_trnQ-UUG, trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnF-GAA_ndhJ, ndhK_ndhC, accD_psaI, petA_psbJ, and ndhF_trnL-UAG (Fig. S1). Most of the DNA sequence variation in Engelhardia species occurred in non-coding regions such as gene spacer region and gene intron region, and the sequence differentiation between LSC and SSC region was significantly higher than that in IR region (Figs. S1-2). By analyzing the boundary differences of and IRb sequences in plastomes of Engelhardia, it was found the inner boundary differences were small. There was no large regional expansion and shortening of spacer regions occurred, which was consistent with the conserved character of platomes within this genus (Fig. 2). The ycf1 gene in all species spanned the SSC/IRa region, with the length of ycf1 in SSC is 4623 bp-4729 bp, and that in IRa is 1004 bp-1104 bp. The pseudogene (Ψycf1) was formed at the corresponding position near the IRb/SSC boundary, and the extension of the short Ψycf1 fragment into the SSC region was observed in all Engelhardia species. Similar to most plants, the ndhF gene involved in photosynthesis was located in the SSC region. The overlapping of Ψycf1 and ndhF has only been detected in E. anminiana, E. spicata and E. villosa. The rps19 gene spanned the LSC/IRb regions in all the Engelhardia species, and it formed a pseudogene (Ψrps19) at the IRa/LSC boundary (Fig. 2). Repetitive sequences in Engelhardia plastomes Plastid genome repeats include dispersed repeats and tandem repeats. Dispersed repeats are further divided into four types: forward, reverse, complement and palindromic repeats.

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: The local parental populations had the highest harvest mass in all cases, showing beneficial effects of local adaptation on performance. speciation describes the process in which populations become reproductively isolated by divergent natural selection (Hatfield and Schluter 1999; Rundle and Nosil 2005). The presence of ecologically dependent postzygotic isolation is therefore consistent with the predictions of speciation resulting from divergent natural selection. This occurs when hybrid genotypes display phenotypes that are intermediate between the optimum phenotype of either parent and as such display lower fitness in the two parental habitats (Hatfield and Schluter 1999). Reciprocal backcross genotypes are fundamental to isolating environmentally dependent fitness effects from those arising from intrinsic genetic incompatibilities: backcross genotypes are more genetically similar to one of the parents, and therefore should have relatively high fitness in the environment of that parent they are more similar to (Rundle and Whitlock 2001). While there are a number of studies that support a link between local adaptation to reproductive isolation (Nagy and Rice 1997; Hall and Willis 2006; Lowry et al. 2008), few studies have measured the relative fitness of backcross genotypes in the wild, a result that is crucial to isolating the effects of divergent natural selection on populations with the potential to interbreed (Rundle and Whitlock 2001). Our work here uses a method to make distinction between ecologically dependent and nonecologically dependent RI, which builds on a growing body of evidence from insects (Egan and Funk 2009; Kuwajima et al. 2010; McBride and Singer 2010) and fish (Rundle 2002; Fuller 2008) to show that ecological reproductive isolation is a potentially important driver in the divergence of plant populations in the wild. Ecological factors have been implicated in previous work on the origins of ecotypes in the S. lautus species complex (Roda et al. 2013b; Melo et al. 2014). The repeated parallel divergence of Dune and Headland ecotypes in the system is a pattern best described by the action of natural selection driving adaptation to these two environment types (Roda et al. 2013a). Head, the signature of ecologically dependent reproductive isolation was present across two components of fitness, establishment, and survival. There was a strong signature of local adaptation in parental genotypes and backcross fitness was higher when the backcross was in the direction of the local genotype.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: 2017;120:6-16. . Hypoglicemic and hypolipedimic effects of Ganoderma lucidum in streptozotocin-induced diabetic rats. Medicines. 2018;5:78. . Structure-activity relationships of lanostane-type triterpenoids from Ganoderma lingzhi as alpha-glucosidase inhibitors. Chem Lett. 2013;23:5900-3. . Lanostane triterpenes from the Tibetan medicinal mushroom Ganoderma leucocontextum and their inhibitory effects on HMG-CoA reductase and a-glucosidase. J Nat Prod. 2015;78:1977-89. . A novel polycyclic meroterpenoid with aldose reductase inhibitory activity from medicinal mushroom Ganoderma leucocontextum. J Antibiot. 2017;70:915-7. . Hypoglycemic activity of Grifola frondosa rich in vanadium. Elem. 2009;131:186-91. . Hypoglycemic effect of extract of Hericium erinaceus. J Agric. 2005;85:641-6. . Hypoglycemic effect of polysaccharides produced by submerged mycelial culture of Laetiporus sulphureus on streptozotocin-induced diabetic rats. Eng. 2010;15:173-81. . Hypoglycemic effect of a Lentinus edodes exo-polymer produced from a submerged mycelial culture. Biochem. 2002;66:937-42. -. Lentinus edodes exposure before and after fetus implantation: Materno-fetal development in rats with gestational diabetes mellitus. Nutrients. 2019;11:2720. . Hypoglycemic effect of Lentinus strigosus (Schwein. ) Fr. crude exopolysaccharide in streptozotocin-induced diabetic rats. J Med Food. 2008;11:513-7. . A polysaccharide isolated from Cordyceps sinensis, a traditional Chinese medicine, protects PC12 cells against hydrogen peroxide-induced injury. Life Sci. 2003;73:2503-13. .

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: REPuter software identified 2,368 repeated sequences, including 24–47 forward repeats, 7–16 reverse repeats, 21–31 palindromic repeats, 1–4 complement repeats, and 89–163 tandem repeats, in the 13 Engelhardia plastomes (Table S4-5, Fig. 3). Most of the repetitive sequences existed in non-coding regions such as IGS and introns (Tables S4–5). Overall, tandem repeats were more prevalent in Engelhardia, accounting for about 60. 52% of all repeat types. On the contrary, the complement repeats were relatively small, accounting for 1. 01% (Table S5). Simple sequence repeats (SSR) have been selected as ideal genetic markers in plant molecular studies due to their high variability [26]. In this study, statistical analysis of SSR was performed by MISA online software, and a total of 1530 SSR loci were detected in the 13 Engelhardia plastomes. The total number of SSRs varied little among individuals, ranging from 111 (E. roxburghiana_JFL02) to 127 (E. villosa). The majority of these plastid SSR (ptSSR) were mono-nucleotide repeats, accounting for 71. 24% of all SSR, followed by di- (13. 07%), tri- (5. 69%), tetra- (4. 97%) and trinucleotide repeats (4. 64%), while hexanucleotide repeats was the least, accounting for only 0. 39% (Table S5, Fig. 3). The A/T type mononucleotide was the most abundant SSR, accounting for 98. 44%, and only 17 G/C single nucleotide repeats were detected, which also resulted in the enrichment of A and T in the plastomes. Most SSRs were located in the LSC region (72. 88%), and a smaller percentage of SSRs were distributed in the SSC (19. 67%) and IR (7. 45%) regions, respectively. Furthermore, most of the SSRs (87. 84%) were distributed in the IGS and introns, while only 12. 16% in the coding sequences (Table S4-5, Fig. 4).

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: This is consistent with evidence from insects (Presgraves and Noor 2002) and plants (Moyle et al. 2004; Scopece et al. 2008), where the initial barriers to gene flow between diverging populations arise due to extrinsic postzygotic isolation, and the strength of postzygotic isolation increases with genetic distance between taxa (Coyne and Orr 1989). Observation of extrinsic barriers during early points on the speciation continuum and the absence of clear intrinsic barriers, as outlined here in Senecio, is also a strong indicator of speciation driven by divergent natural selection. This model contrasts with those where speciation is driven by intrinsic factors and extrinsic barriers arise at later stages along the speciation continuum (Seehausen et al. 2014). While ecologically dependent postzygotic isolation is a fundamental prediction of ecological speciation theory, few empirical examples exist where the specific barriers are isolated from other forms of reproductive isolation. We show in this work that multiple fitness measures across life-history stages show patterns of ecologically dependent postzygotic isolation. Further, these patterns are consistent between replicate ecologically divergent parapatric populations, and the strength of these barriers increases with the degree of evolutionary divergence between populations. Whether this form of ecologically based reproductive isolation will facilitate the evolution of other barriers in the future remains an open question. Our work suggests that the underlying mechanisms of ecological speciation may be contribute to evolutionary divergence within the Senecio lautus species complex and provide a robust example of how ecological differences between populations can lead to reproductive isolation. 10. 5061/dryad. 17h0t. . I. 1966. complex in Australia. 3. Genetic system. Aust. J. Bot. 14:317–330. 2015. The origins of reproductive isolation in plants. N. Phytol. 207:968–984. 2015. Evolutionary and ecological functional genomics of Senecio lautus leaf shape natural variation. School of Biological Sciences. of Queensland, Queensland, Australia. 2013. A practical guide to measuring local adaptation. Ecol. Lett. 16:1195–1205. 1989. Patterns of speciation in Drosophila. Evolution 43:362–381. 2004. Speciation. Sinauer, Sunderland, MA. 2007. Incipient speciation by divergent adaptation and antagonistic epistasis in yeast.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: Hypoglycemic effects of exopolysaccharides produced by mycelial cultures of two different mushrooms Tremella fuciformis and Phellinus baumii in ob/ob mice. Biotechnol. 2007;75:1257-65. . Isolation, purification, and structural features of a polysaccharide from Phellinus linteus and its hypoglycemic effect in alloxan-induced diabetic mice. J Food Sci. 2014;79:H1002-10. . Protective effects and possible mechanisms of ergothioneine and hispidin against methylglyoxal-induced injuries in rat pheochromocytoma cells. Cell Longev. 2017:2017:4824371. . Protein glycation inhibitors from the fruiting body of Phellinus linteus. Bull. 2008;31:1968-72. . a-Glucosidase and aldose reductase inhibitory activities from the fruiting body of Phellinus merrillii. J Chem. 2011;59:5702-6. . Antihyperglycemic effect of polysaccharide from fermented broth of Pleurotus citrinopileatus. Biotechnol. 2006;70:107-13. . Hypoglycemic activity of aqueous extract of Pleurotus pulmonarius in alloxan-induced diabetic mice. Pharm Biol. 2006;44:421-5. . Evaluation of antidiabetic activity of Pleurotus pulmonarius against streptozotocin-nicotinamide induced diabetic wistar albino rats. Biol Sci. 2020;27:913-24. . Pleurotus tuber-regium polysaccharides attenuate hyperglycemia and oxidative stress in experimental diabetic rats. Med. 2012:2012:856381. Yamamoto K, Kimura T. crispa (hanabiratake) ameliorates plasma levels of adiponectin and glucose in type 2 diabetic mice. J Health Sci. 2010;56:541-6. . Effect of a polysaccharide (TAP) from the fruiting bodies of Tremella aurantia on glucose metabolism in mouse liver. Biochem. 2000;64:417-9. .

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Comparative analysis of genomic variation in the Carya, Engelhardia, and Juglans plastomes Comparative analysis of nucleotide polymorphisms of Carya, Engelhardia, and Juglans plastomes, the variability in Engelhardia is higher than that of Carya and Juglans (Fig. 5). There were eighteen hypervariable regions in Engelhardia with Pi > 0. 010 were trnH-trnK, trnK-rps16, rps16-psbK, trnG-atpI, rpoB-trnT, trnT-psbD, psbC-trnM, rps4-trnT, trnL-ndhJ, ndhC-trnV, petA-psbJ, psbE-rpl33, rps11-rps8, rps3-rpl2, trnN-ndhF, ndhF-ccsA, ndhA and ndhH-ycf1, while there were only seven and eight hypervariable regions in Carya and Juglans, respectively. Among them, trnK-rps16, ndhF-rpl32, and ycf1 were common high variation hotspots in these three genera (Fig. 5). Using R. chiliantha as a reference, we characterized genomic variations including single nucleotide variants (SNVs), insertions and deletions (InDels) in the plasomes of Juglandoideae and Engelhardioideae and found that they were very different among different species (Table S6a). A total of 115213 SNVs, 9502 insertions (1–274 bp) and 10428 deletions (1–2,468 bp) were identified in all the collected species (Table S6d). The number of SNVs, deletions and insertions per kb varied at the plastid genome level, with the average values of 15. 03, 1. 36 and 1. 24 in Juglandaceae, 11. 84, 1. 04 and 0. 93 in Carya, 17. 48, 1. 48 and 1. 64 in Engelhardia, and 17. 20, 1. 70 and 1. 28 in Juglans, respectively.

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: Figures AbstractThe mitochondrial genome plays a crucial role in the balance of energy and heat production in organisms and, thus, may be under natural selection due to its potential role in adaptive divergence and speciation. Here, we studied natural selection on the mitogenome of Acrossocheilus (Cypriniformes: Cyprinidae), a genus of fish that inhabits a broad latitudinal distribution ranging from the tropics and subtropics through temperate regions. Specifically, we used 25 published mitogenome sequences of Acrossocheilus species to investigate phylogenetic relationships in this genus and detected signals of positive selection on 13 protein-coding, mitochondrial genes. We found that relaxed purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, we also found evidence of diversifying selection on some codons, indicating episodes of positive selection. Additionally, we analyzed the mitogenomic data within an environmental modeling framework and found that the Ka/Ks ratio of ATP6 may correlated with a mean diurnal temperature range (p = 0. 0449), while the Ka/Ks ratio of COX2 may correlated with precipitation during the driest month (p = 0. 00761). These results suggest that the mitogenomes of Acrossocheilus species may be involved in evolutionary adaptations to different habitats. Based on this, we believe that our study provides a new insight into the role of the mitochondrial genome of Acrossocheilus species in adaptation to different environments. During our study, we also discovered several cases of paraphyly and polyphyly among accessions of species and their putative synonyms. Thus, our study suggests that a careful reassessment of the taxonomy of Acrossocheilus is using high-quality molecular data merited. Citation: (2022) Natural selection drives the evolution of mitogenomes in Acrossocheilus. 17(10): e0276056. Bi-: May 26, 2022; Accepted: September 27, 2022; Published: October 13, 2022Copyright: © 2022 Zhao et al. This is an open access 6. 06 [17]. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 1. Details of the sequences used in this study.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: Meetings with Forays with Fungi across Hemispheres by University of Chicago Press, 2023Cloth: 978-0-226-82963-0 | Electronic: 978-0-226-82964-7DOI: 10. 7208/chicago/9780226829647. 001. 0001 of (cloth, ebook) whirlwind journey through fungus frontiers that underscores how appreciating fungi is key to understanding our planet’s power and fragility. What can we learn from the lives of fungi? Splitting time between the northern and southern hemispheres, ecologist ensures that she experiences two autumns per year in the pursuit of fungi—from Australia’s deserts to Iceland’s glaciers to America’s Cascade Mountains. with Remarkable Mushrooms, we journey alongside Pouliot, magnifiers in hand, as she travels the world. as our guide, we smell fire-loving truffles that transform their scent after burning to lure mammals who eat them and, ultimately, spread their spores. We spot the eerie glow of the ghost fungus, a deceptive entity that looks like an edible oyster mushroom but will soon heave back out—along with everything else in your stomach—if you take a bite. And we crawl alongside vegetable caterpillars, which are neither vegetable nor caterpillar but a fungus that devours insects from the inside out. Featuring stunning color photographs of these mycological miracles, Meetings with shows that understanding fungi is fundamental for harmonizing with the natural world. is an ecologist and photographer with a passion for fungi. "[Meetings with Remarkable Mushrooms] is a joy to read. " — | author of "City of Trees" "Sensual and scientific. Dazzling and boundary breaking. [Meetings with Remarkable Mushrooms] will make you see the world anew. " — Woon | author of "Through the Woods" "The world of fungi is our world even if we don’t know it and can’t see most of it—strange, dazzling, spooky, unpredictable, friendly, deadly, sly. is the perfect guide. She surprises and informs, delights and warns; makes you wish you could walk with her and her passionate companions. That’s OK. In this book you do.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: In terms of these three types of genomic variation, the IR regions presented the fewest numbers per kb, with the average values of 1. 71, 0. 15 and 0. 09 in Juglandaceae, 1. 81, 0. 13 and 0. 11 in Carya, 1. 66, 0. 20 and 0. 10 in Engelhardia, and 1. 70, 0. 14 and 0. 05 in Juglans, respectively. The LSC regions exhibited the maximum numbers of SNVs, deletions and insertions per kb with the average values of 9. 04, 0. 97 and 0. 93 in Juglandaceae, 6. 17, 0. 70 and 0. 63 in Carya, 10. 62, 1. 01 and 1. 23 in Engelhardia being, and 11. 30, 1. 30 and 1. 04 in Juglans (Table S6b). These results collectively indicate that the IR regions were more conserved than the single-copy regions. All genomic structural variations were mapped onto a phylogenetic tree constructed based on the plastid genome, with very different times of insertion events and deletion events occurring in Carya (insertion events: 132–199 times; deletion events: 135–236 times), Engelhardia (186–364; 155–311), and Juglans (149–230; 192–331). It can be concluded that the structural variation of Carya was less than that of Engelhardia and Juglans. The range of structural variation among Engelhardia species was relatively large, especially in E. serrata and E. villosa, with 329 insertions and 306 deletions in E. serrata, and 364 insertions and 311 deletions in E. villosa (Fig. S3). The corresponding genomic positions of these identified InDels were mapped and located into these plastomes of Juglandoideae and Engelhardioideae.

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: Analysis of positive selection To investigate whether positive or purifying selection had occurred at the protein level, we calculated the ratio of nonsynonymous (Ka) to synonymous (Ks) (Ka/Ks > 1, positive selection; Ka/Ks = 1, neutrality; Ka/Ks < 1 negative or purifying selection) using the alignment of the 13 protein-coding genes of Acrossocheilus species. Thereafter, we determined the average pairwise Ka/Ks between sequences for each gene in FEL (Likelihood) implemented on the Datamonkey server ( In addition, we used phylogeny-based methods to detect signatures of positive selection at the codon level [24]. This approach facilitates identifying possible positive selection on a small number of codons within genes that may otherwise be masked by strong purifying selection. Specifically, we applied our reconstructed ML phylogenetic tree in CodeML of the PAML4 package [25] to perform a ML analysis of positive selection on codons. For the analysis, we compared several pairs of null and alternative models (M7 vs. M8, M1a vs. M2a, and M8a vs. M8) using a likelihood ratio test (LRT) to determine whether there are variable ratios of ω at particular codon positions [25] (S1 Table). These codon substitution models, which can be compared using likelihood-ration test, assume that the ω ratio is the same across branches of the phylogeny but different among sites in a multiple sequence alignment. We can identify positively selected codons if M2a (positive selection) provides a better fit than M1a (nearly neutral), or if M8 (beta and ω > 1) provides a better fit than M7 (beta) or M8a (beta and ω = 1). The M7 vs. M8 comparison offers a very stringent test of positive selection [26], while the M8a vs. M8 comparison yields fewer false positives [27]. In addition to testing models in we used HyPhy [28] implemented on the web-server Datamonkey [29] to infer codons under selection according to the following approaches: Bayesian AppRoximation (FUBA) [30], Model of Evolution (MEME) [31], (SLAC), and Fixed-(FEL) [32].

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: " — | songwriter "An evocative, accessible and important book about one of the most vital, yet hugely ignored, kingdoms on our planet—fungi. After reading this you cannot help but see the world in a different light—and should approach mushrooms and truffles with new relish. " — | author of "Call of the Reed Warbler" "Anyone who has joined Alison in a forest, anywhere in the world, will know her incredible ability to magnify those microscopic organisms that hold our natural world together, to connect every element of human life—physical, emotional or social—to the function of our natural landscapes. [Meetings with Remarkable Mushrooms] is like a walk in the forest, pungent and complex, filled with curiosity and wonder, and leaving you with a sense that there is so much more to uncover. " — | ABC-TV "Gardening Australia" "This subterranean journey introduces the quirks of behavior that allow fungi to spread through soils, support living plants, and recycle the debris of nature. Alison is an accomplished storyteller. " — Nicholas P. Money | "The underground teaches us a different language—and is the perfect translator. " — | Amsterdam "[Meetings with Remarkable Mushrooms] takes storytelling about fungi to a captivating new level. A well-researched page turner. " — | of "In this captivating study, ecologist Pouliot expounds on mushrooms she’s encountered during her fieldwork. . . . The result is an enjoyable tour of the fungal kingdom. " — Publisher's Weekly "Conveying an impassioned message for conservation and awareness, Meetings with is a compelling, enlightening look at lowly but remarkable fungi that are often hidden in the shadows. " — “Pouliot conveys the otherworldly charisma of mushrooms with love and skill. ” — “I was entertained and enthralled reading this book and I promise I have never read a book from cover to cover on fungi before. I didn't think it was my jam, but [it turns out] it should be everyone's jam. Fungi is literally the glue that keeps us together. ” — Readings “Pouliot is a mycologist whose knowledge of fungi is extraordinarily vast and intricate.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: It can be found that 90% of InDels were found in intronic (35%) and intergenic regions (55%) for Juglandaceae, 92% of InDels were found in intronic (43%) and intergenic regions (49%) for Carya, 88% of InDels were found in intronic (33%) and intergenic regions (55%) for Engelhardia, and 91% of InDels were found in intronic (31%) and intergenic regions 60%) for Juglans (Table S6c; Fig. 6). Codon usage analysis of Juglandaceae plastomes Comparing the coding sequences of 50 genes with a length over 300 bp of Juglandaceae plastomes, it was found that there were two codons with RSCU value of 1, which are AUG and UGG encoding methionine (Met) and tryptophan (Trp), indicating that the codon usage of two amino acids doesn’t show bias. There were 29 codons with RSCU > 1, of which 16 end with U and 12 end with A, which was the same in Engelhardioideae, Juglandoideae and Rhoipteleoideae. It indicates that the codons ending with U or A are the preferred codons in the plastomes of these three subfamilies. The use frequency and RSCU value of each amino acid in the collected accessions were shown in the Table S7a, Figure S4. There was no significant difference in the codon bias of the genes of most Juglandaceae plastomes. However, the A/T content of the third base in the coding sequence is significantly higher than the G/C content, T3s (0. 4748–0. 4782) > A3s (0. 4399–0. 4438) > G3s (0. 1695–0. 1722) > C3s (0. 1613–0. 1649). We found that Carya ovata and Carya palmeri had the highest values of ENC, GC3s and GC, while Platycarya strobilacea had the lowest values. No significant differences in intra-genus codon p0. 09 and 0.

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: Across all genes, the number of synonymous substitutions was 2. 5–12. 7 times higher than nonsynonymous substitutions, and the Ka/Ks ratios for each gene were all < 1. 0, suggesting signatures of purifying selection (Table 2 and Fig 1). The highest average pairwise nonsynonymous substitutions were in ATP8 and ND6 where Ka/Ks = 0. 123 (Table 2 and Fig 1), and the lowest was found in COX1 with Ka/Ks = 0. 00899 followed by 3, and ND4 (with values between 0. 0184 and 0. 0261) (Table 2 and Fig 1). In general, the ND gene family showed relatively high Ka/Ks compared to other genes. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 1. The Ka/Ks ratios of the 13 different mitochondrial genes in Acrossocheilus species. Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageTable 2. Summary statistics for the Acrossocheilus mitogenome sequences and regions. determined that gene length, nonsynonymous and synonymous mutations, and the total number of mutations were all normally distributed variables based on F-tests. Among these variables, our linear regressions revealed that the total number of mutations and synonymous and nonsynonymous changes were significantly correlated with gene length (Fig 2A, 2B and 2D). Additionally, the number of synonymous mutations showed a significant linear relationship with the number of nonsynonymous mutations (Fig 2C). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFig 2. Correlation analyses. The dots denote the individual values for the 13 different mitochondrial genes in Acrossocheilus species and the line the best-fitted line. (A) Correlation between total number of mutations and length in bases of the genes. (B) Correlation between synonymous mutations and length in bases of the genes. (C) Correlation between nonsynonymous and synonymous mutations. (D) Correlation between nonsynonymous mutations and length in bases of the genes. Phylogenetic analysis The ML phylogeny shows strong support for all relationships (bootstrap value ≥ 95, Fig 3). Acrossocheilus monticola and A. yunnanensis formed a clade as did A. longipinnis and A. iridescens.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: ” — Paper “Powerful stuff, which should be read by all those who continue to support the insane logging of our native forests. ” — | author and environmental activist "wryly describes her companions and their forays into forests, the fungi that inhabit them emerge as her protagonists…. Attending also to the prominent women (including Beatrix Potter) who helped found mycology as a science and fungi’s place in habitat conservation, Pouliot delivers a charming, informative presentation of a world beneath our feet. " — Booklist "[Pouliot makes a] convincing case. . . Fungi are essential to the world as we know it. " — Review of Books "So—do we really need another book about mushrooms? The answer is yes, but only if it’s this one. has written a lovely book that digs deep but wears its learning lightly, and manages to cover—in a series of relatively short, readable, enjoyable and accurate 10. 7208/chicago/9780226829647. 003. 0001[scientific nomenclature;scientific names;common names]Describes how terminology for naming organisms and scientific nomenclature are used throughout the book. Discusses the use of both scientific names and common names in the book. Stirrings in the SubterrainDOI: 10. 7208/chicago/9780226829647. 003. 0002[Kingdom Fungi;fungal awakening;fungal turn;mycophobia;mycophilia;mycelium]This 10. 7208/chicago/9780226829647. 003. 0003[mycelium;hyphae;symbioses;mycorrhizas;ectomycorrhizas;arbuscula mycorrhizas;lichen;saptrotroph;parasite;Pacific Northwest]The concept of mycelium and how fungi function in forests is explored through a trip to the rainforests of the in America's Pacific Northwest. The life cycle of a fungus, the growth of hyphae to form the fungus mycelium, and how fungi differ from animals and plants is explained. Symbioses, especially mycorrhizas are explored, both ectomycorrhizas and arbuscular mycorrhizas.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: 31, psbA, rbcL and psbD with the highest CAI value, and rpl20, rpl18 and rps8 with the lowest one. Most of the CBI values ranged from − 0. 23 to 0. 23, the highest were psbA, psbD and rbcL, and the lowest were ndhF, ndhG and rps14. Most of the Fop values were between 0. 26–0. 55, the highest were psbA, psbD and rbcL, and the lowest were ndhG, ndhF and petD. Most of the ENC value were concentrated between 35. 71and 60. 6, the highest were ycf3, ycf2 and rpl2, and the lowest were rps18, petD and rps14 (Table S7c). The highly expressed genes in the plastid genome of three subfamilies were ycf2, rpoC1 and rpoC2, and the low expressed genes are rps18, petD and rps14 (Table S7d). Combined with the 29 high-frequency codons with RSCU value > 1 in Table S4a, 10 common optimal codons were finally determined, which were and all end with A or U (Table S7d). There was a positive correlation between the codon preference index (CBI) and the optimal codon usage frequency (Fop), and the highest correlation coefficient of 0. 97. The correlation coefficients between CAI and CBI and between CAI and Fop were also higher, which were 0. 72 and 0. 76, respectively, showing a positive correlation. In addition, there were negative correlation between T3s/C3s, T3s/A3s, T3s/G3s, T3s/GC3s, T3s/GC, C3s/A3s, C3s/G3s, A3s/G3s, A3s/CAI, A3s/CBI, A3s/Fop, A3s/ENC, A3s/GC3s, A3s/GC, G3s/CAI, G3s/CBI, G3s/Fop, CAI/GC, etc.

Output: pass


Input: Claim: Natural selection drives the evolution of species through differential survival. [SEP] Text: A positive correlation between an environmental variable and Ka/Ks ratio for a specific mtDNA gene may suggest that species inhabiting similar environments undergo convergent adaptative processes for that gene, and that the processes are divergent in different environments. Environments with high energy demands, such as extreme climates, are typically associated with stronger functional constraints on metabolism; that is, lower Ka/Ks values associated with codons/genes linked to energy metabolism [45]. This is consistent with our findings that the Ka/Ks values for ATP6 and COX genes are generally low relative to those of ND genes as the former two genes were found correlated with specific environmental variables, while the latter were not. revealed some significant amino acid changes affecting the equilibrium constant in both ATP6 and COX2 as well as the alpha-helical tendencies for COX2, even though we did not detect any sites of positive selection in this gene has been found in other pelagic fish [46]. Thus, mutations observed in ATP6 of Acrossocheilus could be related to relaxed purifying selection. In contrast, codon 186 was detected as a possible site of positive selection in COX2 in the MEME analysis. The COX2 gene is a catalytic subunit of complex IV of the and plays a role in increasing the coupling efficiency to produce ATP and, consequently, heat. Positively selected sites that appear to interact with other COX subunits (complex IV) have been reported from other fish, such as Scombroidei [11, 46]. Overall, the correlation between precipitation-related variables and Ka/Ks value for COX2 could be because frequent rains reoxygenate waters [47], thereby increasing the dissolved oxygen available for ATP production. Although we detected several significant correlations between Ka/Ks ratios and environmental variables, we cannot reject the possibility that these results are influenced by other variables not evaluated here, such as salinity. ConclusionHere, we identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of Acrossocheilus species to their environment. This is a novel study to comprehend adaptation to the environment occurring at a molecular level. Integration of environmental and molecular data provide insights into how Acrossocheilus species have adapted to their environments and therefore how they may respond to future, human-induced changes to their environment. Supporting informationS1 Table. Details of site models used in CodeML. S2 Table.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: The author then heads to the glaciers of Iceland to look at the oldest known fungal symbiosis, that of lichens. Other fungus trophic modes such as saprotrophs and parasites, in particular how they break down wood and convert it to soil and the process of decay, is discussed in the context of an Iceland forest. Into the Australian BushDOI: 10. 7208/chicago/9780226829647. 003. 0004[Wurrung;Yorta Yorta;Dhungala;ethnomycology;Maori;o Nga Harore;hekaheka;Aetearoa]This 10. 7208/chicago/9780226829647. 003. 0005[microfungi;rusts;smuts;history of mycology;Honey Fungus;Coral;fungal disease;pathogen]Fungi have traditionally been misunderstood in many cultures due the sudden and seemingly inexplicable appearance of mushrooms and subsequent disappearance, among other reasons. The history of mycology in Australia, which was directly linked to agriculture and began with the appointment of an agricultural scientist to investigate pathogenic microfungi, specifically fungal rusts and smuts that infect crop monocultures, especially cereal grains, set a particular foundation that influenced how fungi are regarded today. The author explores how agriculture and horticulture have focused almost solely on pathogenic fungi while ignoring the great benefits provided by most fungi, and the paradox that industrialized agriculture perpetuates 'fungal diseases'. Perceptions of fungi are also influenced by language and the dearth of appropriate terms and phrases to describe and discuss fungi is especially apparent in English. The scapegoating of fungi as the cause of environmental problems, rather than a symptom of larger changes in environments, is explored through the spread of the (Armillaria mellea) in a Swiss forest. The saga around a second fungus, the Coral is investigated through the response to its recent discovery in Australia. Fungi, Fire, and IceDOI: 10. 7208/chicago/9780226829647. 003.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Among them, A3s/CAI has the highest degree of negative correlation, with a correlation coefficient of -0. 57 (Fig. S5). The results of three subfamilies were similar to the whole Juglandaceae family, with the highest correlation coefficients being CBI and Fop, followed by the correlation coefficients between CAI and CBI, as well as between CAI and Fop (Fig. S5). The ENC values were positively correlated with T3s, C3s, G3s and GC3s. However, ENC values were negatively correlated with A3s. ENC values can be used to determine the relative expression levels of genes [27], and our results showed that the content of the third base of synonymous codons is closely related to gene expression levels, and T3s, C3s and G3s are positively correlated with gene expression, while A3s was negatively correlated with gene expression (Table S7e, Fig. S5). ENC values for all screened gene coding sequences ranged from 35. 71 to 60. 6. The ENC frequencies were calculated using the formula (ENCexp-ENCobs)/ENCexp, ranging from − 0. 25 to 0. 28. There were 2051 ENC frequencies in the range of -0. 1 to 0. 1, which were close to the expected ENC values (Table S7f). Based on the standard curve formula ENC = 2 + GC3 + 29/[GC32+(1 − GC3)2], we took ENC as the ordinate and GC3s as the abscissa to draw a scatter plot (Fig. 7). It can be seen that most of the genes are located on or near the standard curve (Fig. 7A), indicating that the expected ENC value and the actual value of most genes is nearly uniform, and the mutation has a greater impact on the codons bias of coding gene. However, we also found the observed ENC values of six genes (rpl16, rps18, cemA, psbA, rps14, and ycf3) in all species deviated significantly from the standard curve (Fig. 7A, B). Among all genes, ycf3 showed the highest ENC value, while rps18 and rpl16 showed the lowest ENC value (Fig. 7B; Table S7f).

Output: pass


Input: Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Related research -of the environment on horizontal gene transfer between bacteria and archaea View 10. 7717/peerj. 3865 Published 2017-09-29 Accepted 2017-09-08 Received 2017-04-06 gene transfer, Archaea, Temperature, Oxygen utilization, Genome-size correction, © 2017 Fuchsman et al. is an open access 2017. Effect of the environment on horizontal gene transfer between bacteria and archaea. PeerJ 5:e3865 Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e. g. , the nutrient regime for which it is adapted). investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria.

Output: corroborate


Input: Claim: Mushrooms are the only type of fungi studied by mycologists. [SEP] Text: 0006[climate change;pyrophiles;hidden pinkgill;Pam Catcheside;alpine;Swiss Alps;Federal institute for Forest, Snow and Landscape Research;fire]Like flora and fauna, many fungi are adapted to cope with extremes of weather and climate. However, our rapidly changing climate is pushing many species to the limits of their survival. This 10. 7208/chicago/9780226829647. 003. 0007[ghost fungus;Cordyceps;lobster mushroom;Pacific Northwest]In this 10. 7208/chicago/9780226829647. 003. 0008[mycophagist;invertebrate;springtails;Lynne Boddy;hypogeous fungi;truffle fungi;shifting baseline syndrome;Cantharellus;Lorelei Norvell]Animals that eat fungi are known as mycophagists. This 10. 7208/chicago/9780226829647. 003. 0009[biodiversity;conservation;flagship species;waxcaps;conservation status;of Threatened Species;Red List;Peter Buchanan;blue pinkgill]This 10. 7208/chicago/9780226829647. 003. 0010[Yol? u;European Renaissance;women in mycology;ergot;witch-hunting;Age of Enlightenment;Beatrix Potter;Suzanne Simard;mycology]Women have long been involved in mycology, as collectors, illustrators, researchers, as those who prepared specimens for herbaria, mostly in honorary positions, but also as mycologists. Yet most are poorly known. This 10. 7208/chicago/9780226829647. 003. 0011[logging;land restoration;Landcare;disturbance;agriculture;forestry;Sue Brunskill;Kazuko Yamamoto;care]This 10. 7208/chicago/9780226829647. 003. 0012[subterranean networks;fungi;mushrooms]The book ends with a gathering around the campfire, reflecting on all the fungi, places, experiences, and people that feature in the book, and how the subterranean networks of fungi inspire innovative ways to imagine the future.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: PR2-plot is used to analyze the composition of the four bases at the third position of the codon encoding the amino acid, plotting with G3/(G3 + C3) and A3/(A3 + T3) as the horizontal and vertical coordinates. When the four bases are evenly distributed, codon bias is not affected by mutation and natural selection [28]. The results showed that A/T and G/C (pyrimidine versus purine) were used slightly differently at the third codon position in the protein-coding sequence of Juglandaceae (Fig. 7C). The PR2-plot shows that there is a slight imbalance in the use of A/T and G/C at the third codon of the CDSs of 36 Juglandaceae plasomes, especially the four CDSs (psbA, rpl20, rpl16 and rps8) (Fig. 7C). The number of genes in the third and fourth quadrants is more than that in the first and second quadrants, and the number of genes distributed in the fourth quadrant is greater than the number of genes distributed in the other three quadrants, so G and T are used most frequently (Fig. 7C). Selective pressure analysis of CDS in analyze the evolutionary pressure among the protein coding sequences of 8 Juglandaceae species, the Ka/Ks value of 80 protein coding sequences (CDS) were calculated. The results showed that the Ka/Ks values of 78 genes was almost all less than 1, indicating that most genes were subjected to purifying selection (Fig. 8C, Table S8a). Only rpl22 and psaI have Ka/Ks > 1, indicating that positive selection happened during plastome evolution in Juglandaceae and three subfamilies. We also found that rps16 was only subjected to positive selection in Juglandaceae and Engelhardioideae. For all Juglandaceae samples, the Ka/Ks values of photosynthesis-related genes were significantly lower than those of self-replication-related and other genes, indicating stronger purification selection (Fig. 8A, Table S8b). For functional classification genes, except for differences in photosynthesis related genes between Engelhardioideae and Juglandoideae, other Ka/Ks values showed no significant differences (Fig.

Output: pass


Input: Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters. gene transfer (HGT) is an essential aspect of microbial evolution, but its mechanisms, rates, and consequences are poorly understood and difficult to quantify (Boto, 2009). Some organisms are more likely to engage in horizontal gene transfer than others. For HGT to occur, the transferred DNA has to be incorporated into the genome after uptake. For this reason, HGT is more common among closely related organisms (Kloesges et al. , 2011). Intra-domain gene transfer seems to have been particularly important in bacterial evolution (Wolf et al. , 2012). However, HGT does occur between archaea and bacteria and is more easily detected in such cases. Since the apparatus for transcription and translation are significantly different between archaea and bacteria, only transferred genes with strong benefits would be retained in their new genome, as their initial expression is likely to be low (Lawrence & Hendrickson, 2003). There is abundant evidence of HGT of key genes between bacteria and archaea adapted to live in similar environments: hot acid (Fütterer et al. , 2004), acid mine drainage (Guo et al. , 2015), extremely high salt (Mongodin et al. , 2005), marine (Frigaard et al. , 2006; Brochier-Armanet et al. , 2011), high mercury (Barkay et al. , 2010), and high temperature (Rhodes et al. , 2011). Whether HGT is limited by geography has not been well investigated, but it likely spans oceans and continents. HGT between archaea and bacteria can be accomplished by acquiring free DNA from the environment, which implies greater proximity between the two parties, or by transfer of DNA from viruses or gene transfer agents. A comparison of viral metagenomes across the world’s oceans revealed that viruses are widely dispersed, though there is a relationship between geographic and genetic distance (Angly et al. , 2006).

Output: corroborate


Input: Claim: All amphibians can breathe underwater for their entire lives. [SEP] Text: As the use of inhaled terbutaline by an athlete necessitates a TUE, the third criterion that must be met to approve a TUE, which states that a TUE should not be approved if there is a permitted alternative, needs to be considered. As the pharmacologically similar SABA salbutamol is permitted, this should result in the TUEC rejecting an application from an athlete to inhale the prohibited SABA terbutaline. However, appropriately WADA has acknowledged that it should have no role in prescribing medications for athletes. Hence when an athlete’s recommended inhaled SABA has been terbutaline for some years, WADA accepts that it is unreasonable to demand that the athlete must suddenly switch to inhaling salbutamol and an application to continue to inhale tebutaline should be approved. Glucocorticoids are prohibited only in competitionadvises that the systemic use (e. g. oral or intravenous administration) of GCSs is prohibited and requires a TUE. In contrast, all inhaled GCSs are permitted in sport. Hence the for Asthma’s gold standard for preventive treatment for asthma, EIB and AHR, inhaled GCS can be prescribed without restriction [27]. It is pleasing to note the steady improvement in the prescribing habits of doctors managing Olympic athletes with asthma/AHR, which may reflect improved knowledge of asthma management by sports and exercise physicians and team doctors and/or increased involvement of respiratory physicians (table 2). Table 2Percentage of athletes taking an IBA who were also using an inhaled users taking an inhaled GCSAtlanta 1996#46. 1%Athens 200469. 9%Torino 200677. 2%Beijing 200887. 2%No data were available for games held in 1998, 2000 and 2002. #: In Atlanta, IBA use was by notification only, for the other Games athletes had demonstrated asthma or AHR. Open in new tabMany elite asthmatic athletes have required a course of an oral GCS to manage an acute episode of asthma and have been granted a TUE. When systemic GCSs are used for the treatment of an exacerbation of asthma, a retroactive/emergency TUE should be submitted as soon as possible to the appropriate TUEC.

Output: pass


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: 8C, Table S8c). Phylogenetic analysis of this study, Quercus rubra (Fagaceae) was used as the outgroup, ML and BI trees of Juglandaceae species based on the complete plastome (excluding one copy of the inverted repeat) showed nearly identical topologies (Fig. S6). The phylogenomic results indicated that Juglandaceae family was mainly divided into three groups, including Juglandoideae, Engelhardioideae and Rhoipteleoideae subfamilies, with a very high support rate (BS = 100%, PP = 1). The phylogenomic tree further supported 7 major branches, corresponding to 7 genera, namely the monophyletic and Rhoiptelea. There were two main clades in Juglandoideae, clade I was Carya, clade II were Juglans, Pterocarya, Cyclocarya and Platycarya. In the ML tree, the support rate inside clade I (BS = 63–100%) was lower than that of clade II (BS = 66–100%). The species of Carya were divided into two sects, C. hunanensis, C. kweichowensis, C. sinensis, C. polianei, C. tonkinensis, and C. cathayensis were grouped together, while the remaining 12 species were grouped together. were divided into three sects, namely the Sect. Juglans or Dioscaryon, Sect. Cardiocaryon, and the Sect. Rhysocaryon. The Sect. Juglans/Dioscaryon included J. regia and J. sigillata, while the Sect. Cardiocaryon included J. mandshurica, J. ailanthifolia and J. hopeiensis, the Sect. Rhysocaryon included J. cinerea, J. nigra, J. hindsii, J. major and J. microcarpa. were divided into two sects, one included P. fraxinifolia, P. stenoptera and P. hupehensis, the other included P. macroptera var. insignis and P. tonkinensis.

Output: pass


Input: Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: Though most viruses are specific to either bacteria or archaea, Caudovirales viruses may be able to infect both bacteria and archaea (Prangishvili, Forterre & Garrett, 2006), and little is known about the range of gene transfer agents (McDaniel et al. , 2010). Multiple methods of detecting HGT have indicated that it can be influenced by the lifestyles of the organisms involved. One analysis of recent HGT, as determined by identification of identical 500 nucleotide blocks, indicated that ecology was more important than phylogeny; oxygen tolerance and pathogenicity were identified as the strongest factors (Smillie et al. , 2011). Another study identified several hundred phylogenies of single genes (out of 7,000) that reflected the lifestyles of the organisms rather than their taxonomy (Schliep et al. , 2011). For example, in 597 gene trees, hyperthermophiles and non-hyperthermophiles were better discriminated than were archaea and bacteria (Schliep et al. , 2011). Rhodes et al. (2011) also detected increased transfer between thermophiles. However, when halophilic archaea were examined with the same technique, they appeared to have predominantly exchanged genes with non-halophilic microbes (Rhodes et al. , 2011). It is possible this could be related to an ancient acquisition of 1,000 bacterial genes that caused Haloarchaea to differentiate from methanogens (Nelson-Sathi et al. , 2012). Contrastingly, Gophna et al. (2015) found a negative correlation between growth temperature and gene transfer. In short, evidence indicates that horizontal gene transfer is affected by lifestyle differences, particularly growth temperature, oxygen utilization and pathogenicity. Many similar studies, however, have reported that genome size is the most important factor determining the amount of horizontal gene transfer. In a study utilizing phylogenetic trees to examine HGT in eight genomes, genome size and %GC were the most significant factors determining the number of horizontally transferred genes, rather than more environmentally-relevant factors (Jain et al. , 2003). Presence-absence patterns discordant with species trees have also indicated that large genomes have more horizontally transferred genes than small genomes (Cordero & Hogeweg, 2009; Gophna et al. , 2015). A small genome is an adaptive strategy that allows a microbe to use fewer nutrients and resources.

Output: corroborate


Input: Claim: All amphibians can breathe underwater for their entire lives. [SEP] Text: ERS website you have a myERS account, please click the button above to login. Not sure if your membership is up to date? Check at my. ersnet. org Individual/Login via username/password Login via Shibboleth/Openyour library’s subscribed content or your individual user account above Redeem book access code Register (non-ERS members) 0 items You have 0 items in your shopping cart. Click to view details. Search within ERS publications Main navigationpodcastsERS conference abstractsBooksAll BooksBuy print bookspodcastsusTopicsDoes one size fit all? An update on chronic ventilatory support in different respiratory illnesses João Breathe 2023; 19(2): 230046; DOI: PDF to login to or register for a personal account in order to add favourites. login to or register for your personal account in order to apply a label (tagged)EndNote 8 (xml)link Please login to or register for a personal account in order to receive an alert. Log in or register to access this content This 2. However, because of the possible high cost-effectiveness of the treatment, a follow-up at 6–12 months should be mandatory to verify the achievement of the purpose. After an episode of acute hypercapnic respiratory failureIn this subgroup of patients, two recent studies with similar design showed different results in terms of effect of HNIV on mortality and hospitalisation rate [6, 7]. The most important explanation for the apparently contrasting results was the different timing in enrolment of patients. In the study by Murphy et al. [6], HNIV was shown to reduce the rate of deaths or hospitalisation in patients with persistent hypercapnia 2–4 weeks after the acute phase. On the other hand, by enrolling the patients at the discharge from hospitalisation, as in the study by Struik et al. [7], there is a risk of over-treatment due to possible spontaneous recovery from hypercapnia, as already described by Costello et al. [8]. Similar indications came from the Society guidelines that followed, on HNIV in chronic hypercapnic COPD patients [9], which interestingly highlighted the importance of screening the patient for obstructive sleep apnoea (OSA) before starting HNIV. In fact, the prevalence of overlap with OSA was found to reach 50% in patients coming from an acute exacerbation of COPD [10].

Output: pass