Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: 91 Mya) during the Late Paleocene, and Cyclocarya paliurus at 54. 10 Mya (95% HPD: 50. 84–57. 41 Mya). The divergence of Pterocarya and Juglans was estimated at 46. 29 Mya (95% HPD: 43. 43–49. 63 Mya) during the Middle Eocene. Most genera of Juglandoideae subfamily were diverged between 46. 29 and 64. 98 Mya in the relatively warm and dry climate of the to the (Fig. 9). analysis of Engelhardia plastomes In this study, the plastomes of 13 individuals from eight species Engelhardia were newly sequenced, annotated and compared. The results showed that all species of the Engelhardia had a typical tetrad structure, and the genome sizes were similar, about 161 kb (161,069 bp–162,336 bp), and the GC contents of the plastomes were 35. 8–36. 0%, which were similar to the sequence length and composition of the previously obtained Juglandaceae plastomes [1, 29–31]. By comparison of the GC content of each part of the plastomes of Engelhardia, it was found that the GC content in the IR regions was higher than those of the LSC and SSC regions, and the high GC content is conducive to the stability of the genome, so the conservation of the IR regions may be related to the GC content [32]. Multiple plastomes comparison among all the Engelhardia species using mVISTA and Mauve alignment showed a very good synteny. No inversion or translocation of DNA fragment rearrangement was detected in the sequences, which is consistent with the conservation of the plastomes [33]. By analyzing the boundary differences of and IRb sequences in the plastid genome of Engelhardia, it was found that the boundary differences of plastomes of Engelhardia were small (Fig. 2), which is similar to Carya, with a relatively-conserved pattern of IR boundaries [30]. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the divergence of plant species and details about plastomes, without any mention of artifacts or insights into past cultures. It does not support, contradict, or relate to the assertion about artifacts and cultural insights.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: Proteins in reciprocal best hit files were matched to LPI numbers from DarkHorse for both the bacteria and archaea. If the LPI number was below 0. 2 for either the bacteria or the archaea, the reciprocal best hit was tagged as horizontally transferred (Table S4). For each archaeon, each bacterium with a horizontally transferred gene count more than 1. 96 standard deviations from the mean was defined as significantly enriched in horizontally transferred genes and considered to form an enriched pair with that archaeon. This technique is susceptible to multiple testing issues, but enrichment with three or more archaea is considered robust. Three bacteria were >1. 96 standard deviations from the mean for only one archaea and were not substantiated by enrichment in shared genes (above). These three bacteria were removed from further analysis as potential false positives. COlinking proteins to COGs or Clusters of were downloaded from NCBI ftp site. The COG collection used was originally created in 2003 (Tatusov et al. , 2003) and then used to identify COGs in subsequently sequenced genomes. The numbers of RBH in each category can be seen in Table S5. Fifteen categories had enough shared genes in them to examine statistically. COG categories were examined both with and without removal of the genome size effect. analyses, a four-parameter log–logistic function was fit between bacteria and each archaea for each COG category to remove the effect of genome size, as described above. The removal of the correlation of RBH and genome size was checked for each COG and archaea and was successful in all cases (R2 < 0. 001). Additionally, to further take GC into account, the effect of genome size and GC were simultaneously removed from the residuals for each archaea by multiple linear regression using the number of genes in the bacterial genome, reciprocal BLAST hits, and GC content. (Clarke, 1993) analyses were done with the Primer 6 program ( Results and the 448 bacterial genomes used in this study, 273 are from non-pathogens, 81 were anaerobes, 42 were thermophilic or hyperthermophilic (optimum growth temperature >50 °C; abbreviated as “(hyper)thermophilic”) (Fig. 1; Table S1). Regarding salinity, there were 72 moderately halophilic bacteria and 6 extremely halophilic bacteria (Table S1). [SEP] Justify:

Output: The text supports the claim by discussing a methodology for identifying horizontally transferred genes in bacteria and archaea, indicating that horizontal gene transfer is a significant mechanism for acquiring new traits. The text mentions tagging reciprocal best hits as horizontally transferred and examining pairwise relationships between bacterial and archaeal genomes, emphasizing the importance of horizontally transferred genes in evolutionary studies.


Input: Task: contrast the claim using the given text. Claim: Snakes use their fangs only for defense and never for hunting prey. [SEP] Text: It is clearly written, and nicely illustrated, and the methods and procedures are meticulously documented. Weaknesses: One caveat is that the Nav channels used to test mutations in expression systems are rat channels engineered with TTX-resisting substitutions observed in snake populations. The ideal experiment would have been to use the snake channels. While the rat channels appear to be a good substitute for the snake channels and the authors have taken pains to show that the important amino acids are conserved between garter snakes and rats, the authors might explain why they did not use snake channels. The noise analysis seems like a reasonable way to get at the question of single-channel conductance. But why did the authors not just measure single channel conductance in patches as opposed to this much more complex and roundabout method? It is recommended that the authors discuss how noise analysis deals with the problem of having the number of open channels changing rapidly during activation and fast inactivation. Is this a potential problem for deriving the total number of channels? #3 (Public Review): Summary: This paper explores the cost of toxin resistance in snakes that prey on newts defended by highly potent TTX. Two species of garter snakes, T. atratus and T. sirtalis, are examined. Both species have resistant and sensitive populations. Resistance is achieved by substitutions in the voltage-gated sodium channels, which block TTX binding. Resistant T. atratus carry the triple substitutions EPN while resistant T. sirtalis carry the quadruple LVNV. These substitutions occur on the third and fourth intracellular domains of the voltage-gated sodium-channel gene Nav1. 4, which is the paralog found in skeletal muscle. EPN and LVNV have been previously attributed to conferring resistance to TXX through target-site insensitivity of the channel. Previous work has also shown that snakes from resistant populations have reduced locomotor capabilities compared to their non-resistant counterparts. The authors systematically test the hypothesis that the resistance-conferring substitutions affect other phenotypes related to the function of the voltage-gated sodium channel, which is, in turn, responsible for the reduced locomotor capabilities. First, they compare the effects of EPN and LVNV on recombinantly expressed rat Nav1. 4 with and without EPN and LVNV (in vitro). They find that both EPN and LVNV significantly reduce the channel's conductance. [SEP] Justify:

Output: The text contrasts the claim by discussing the cost of toxin resistance in snakes that prey on newts. It specifically mentions that the paper explores how two species of garter snakes, T. atratus and T. sirtalis, have adapted to prey on toxic newts, indicating that their fangs are used in the context of predation rather than solely for defense.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: In Engelhardia, the ycf1 gene contains two copies, one located at the SSC/IRa boundary is a complete gene, the other located at the IRb/SSC boundary in the form of a pseudogene Ψycf1, which no longer encodes a protein [34]. Likewise, due to the existence of the boundary effect, Ψrps19 existed at the IRa/LSC boundary (Fig. 2). Repeated sequences are ubiquitous in gene sequences and gene intervals, which not only protect the coding sequence [35], but also maintain the stability of the genome. The SSRs of the plastid genome have abundant polymorphic sites and are widely used in molecular markers, variety identification and other studies [36]. The present study examined dispersed repeats and tandem repeats, found that tandem repeats were more common (60. 52%) in Engelhardia. In our study, 24 complement repeats were detected in Engelhardia, this result was consistent with other Juglandaceae species [37–39]. Almost all repeating units of SSRs consist of A and T bases, which is consistent with the previous study by Yi et al. [40]. These plastomes SSRs can provide candidate molecular markers for Engelhardia, which will contribute to population genetics and evolution studies, as well as its molecular breeding and conservation. DNA barcoding is a novel species identification technology that uses standard short gene regions as markers for rapid, accurate and efficient identification of species [41]. Zhang et al. used five plastome regions (psbA-trnH, trnL-trnF, rps16, trnS-trnG, and rpl32-trnL), one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR) were selected for species identification of Engelhardia [9]. In our study, we used the complete plastomes to carry out nucleotide polymorphisms analysis of Engelhardia for more potential molecular markers. The results showed that the IR regions of all species had lower genetic polymorphism than the LSC and SSC regions, and the coding region sequences were more conserved than the non-coding region sequences (Fig. 5), which were similar to the findings of most angiosperms [42]. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses genetic sequences and molecular characteristics of the Engelhardia plant, without any mention of artifacts or insights regarding past cultures. The content focuses on genetic research and species identification rather than cultural analysis.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: After determining shared genes from reciprocal best BLAST hits (Table S2), we explored two ways to predict the expected number of shared genes for each bacterial genome size: (1) the Korbel weighted average that utilizes both archaeal and bacterial genome size and (2) an empirical log–logistic function. While the fits were similar for bacterial genome sizes <5,000 bp, the empirical log–logistic function was superior for genomes >5,000 bp (Fig. S2) so was used for further calculations (Fig. 3, Fig. S1). Here, we denote archaea-bacteria pairs that have significantly more (>2 standard deviations from the mean calculated with the log–logistic function) reciprocal best hits (RBHs) than expected based on genome size to be enriched in shared genes (Table S3). This technique is particularly useful for identifying unusually large numbers of shared genes in bacteria with small genomes. Identifying horizontal gene transfer Genes can be shared between archaea and bacteria either due to horizontal gene transfer or due to vertical inheritance from their common ancestor. To test for the extent to which vertical inheritance can explain the numbers of shared genes between archaea and bacteria, we used a Mantel test to compare a similarity matrix derived from each bacterial genome’s number of shared genes with each archaeal genome to a similarity matrix derived from each bacterial genome’s 16S rRNA genetic distance to archaeal 16S rRNA. The correlation between the two matrices is significant (R = 0. 176 p < 0. 0001), but the R value is not high. This result implies that some, but not all, of the shared genes between archaea and bacteria were inherited from the last common ancestor, which is not surprising. To disentangle vertical inheritance and horizontal transfer, we used the DarkHorse algorithm, which searches for horizontally transferred genes using a probability-based, lineage-weighted method in which the lineage of each gene is compared to the lineage of the entire genome (Podell & Gaasterland, 2007). The phylogenetic distance between bacteria and archaea is very large, so we are only examining genes with extremely large lineage differences from the entire genome, which increases the robustness of our results. By cross-referencing our reciprocal best hit data with the DarkHorse results, we can flag some genes as potentially horizontally transferred (Table S4). [SEP] Justify:

Output: The text corroborates the claim by discussing mechanisms such as 'horizontal gene transfer' that allow genes to be shared between archaea and bacteria, specifically stating that genes can be transferred horizontally or inherited vertically. It details methods like the DarkHorse algorithm used to identify potentially horizontally transferred genes, supporting the idea that horizontal gene transfer is a significant mechanism for bacteria to acquire new traits.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: Correction 27 Aug 2018: (2018) Correction: Response of (Ranidae) to Threats from Predators and Parasites. 13(8): e0203252. View correction Figures AbstractOrganisms are exposed to strong selective pressures from several sources, including predators and pathogens. Response to such interacting selective pressures may vary among species that differ in life history and ecology in predictable ways. We consider the impact of multiple enemies (fish predators and trematode parasites) on the behavior of larvae of three anuran species (Lithobates ( = Rana) sylvaticus, L. clamitans and L. catesbeianus). We show that the three ranid species differ in response to the trade-off imposed by the simultaneous presence of fish predators and trematode parasites in the environment. Two more permanent pond breeders (L. clamitans and L. catesbeianus), which commonly encounter parasites and fish, increased activity when in the combined presence of parasites and a fish predator, resulting in a relatively lower parasite encystment rate. In contrast, the temporary pond breeder (L. sylvaticus), which does not commonly encounter fish in the wild, decreased activity in the combined presence of a fish predator and parasites similar to when only the predator was present. For L. sylvaticus, this suggests that the presence of an unknown predator poses a greater threat than parasites. Further, the presence of fish along with parasites increased the susceptibility of both L. sylvaticus and L. clamitans to trematode infection, whereas parasite infection in L. catesbeianus was unaffected by the presence of fish. Unpalatability to fish may allow some species to respond more freely to attacking parasites in the presence of fish. The results from this study highlight the importance of considering multiple selective pressures faced by organisms and how this shapes their behavior. Citation: (2012) Response of (Ranidae) to Threats from Predators and Parasites. 7(11): e49592. of America Received: August 8, 2012; Accepted: October 15, 2012; Published: November 20, 2012Copyright: © 2012 Szuroczki, Richardson. This is an open-access 1. Response of tadpoles to the presence of parasites and predators and the hypothesized response to the presence of both, which will depend on the relative vulnerability of the tadpole to the predator. [SEP] Justify:

Output: The text contrasts the claim by demonstrating that amphibians, specifically the studied ranid species, exhibit varying behavioral responses to the presence of predators and parasites. For instance, the species L. clamitans and L. catesbeianus increased their activity in the presence of both fish predators and trematode parasites, implying a form of defense mechanism against the threats. Additionally, it discusses how different species adapt their behavior based on the presence of these pressures, highlighting that amphibians do indeed have methods of response to predators.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: However, we still found eighteen hypervariable regions in Engelhardia, including trnK-rps16, ndhF-rpl32, and ycf1, which also were highly variable in Carya and Juglans (Fig. 5). They could be used for species identification of Engelhardia, even for Juglandaceae. Genomic structural variation across plastomes of two subfamilies With R. chiliantha as reference, we characterized genomic variations including SNVs, insertions and deletions (InDels) in the plastid genomes of Juglandoideae and Engelhardioideae. Although they were different among different species (Table S6a), the overall was conserved. By comparing genomic variations in different regions, we found that the IR region has the smallest number of variations per kb (Table S6a), was more conserved than the single copy regions, and genes were more conserved than the intergenic regions, which is consistent with the characteristics of the genome [42]. Localizing these mutations into plastome, it was found that the majority of insertions and deletions were distributed in introns and intergenic regions. The uneven distribution of genomic structural variations in plastids suggested that they may have negative effects and can be easily eliminated through purification selection [43]. Structural variation may not only affect the heterogeneity of genomic structure, but also affect the evolution of protein coding genes in the plastomes of Juglandoideae and Engelhardioideae. By length analysis of InDels in protein coding gene, it was found that only 1200 were multiples of 3 in length among the 3993 InDels in Engelhardia, while there were 1428/5670 and 1248/4764 InDels for Carya and Juglans, respectively. This finding showed that negative selection of frameshift InDels may not truly affect the plastid protein coding genes, which is contrary to the results observed in the six nuclear genomes of other flowering plants [44]. By mapping structural variations to the exons and RNA genes of protein coding genes in the plastomes, the universality of plastid genome structural variations has been further confirmed, suggesting that InDels may be an important driving factor for the evolution of plastid genes in Juglandoideae and Engelhardioideae. [SEP] Justify:

Output: The text does not address the claim regarding artifacts and past cultures. It focuses on genomic variations in plants, specifically discussing plastid genomes and structural variations, which are unrelated to the understanding of daily lives in past cultures through artifacts.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: In general, the numbers of potentially horizontally transferred genes identified by DarkHorse are greater in bacteria that form archaea-bacteria pairs enriched in shared genes (Fig. 4 and Fig. S5). Over half (55%) of the bacteria in pairs with enriched RBHs also had greater than two standard deviations above the mean potential horizontally transferred genes identified by DarkHorse. Figure 4: Comparison of shared and transferred genes. Examples of HGT for anaerobic hyperthermophile Desulforococcus kamchatkaensis (A), anaerobic mesophile Methanosarcina acetivorans (B), aerobic mesophile Nitrosopumilus maritimus (C). In the first column the number of potentially horizontally transferred genes as determined from the DarkHorse algorithm is compared to the number of reciprocal best hits between bacteria and each archaeon. A positive value on the x-axis indicates the RBH count was greater than 1. 96 standard deviations from the mean. In the second column, the number of potentially transferred genes is compared to the number of those genes transferred from archaea to bacteria. In the third column, the number of potentially transferred genes is compared to the number of those genes transferred from bacteria to archaea. Color-coding describes whether the bacterium forms a pair with the archaeon listed (red), with any archaea in this study (blue), or not with any archaea (green). Download full-size image DOI: 10. 7717/peerj. 3865/fig-4 Correlations with growth conditions After the effect of genome size is removed, interesting trends emerge between the number of shared genes and the lifestyles of archaea and bacteria. For example, the enriched archaeal-bacterial pairs involving Desulfurococcus kamchatkensis, an anaerobic hyperthermophilic archaeon, predominately include (hyper)thermophilic bacteria (Fig. 3A). Similarly, Methanosarcina acetivorans, an anaerobic mesophilic archaeon, primarily forms enriched archaeal-bacterial pairs with anaerobic bacteria (Fig. 3B). Contrastingly, the number of archaea-bacteria pairs involving extremely halophilic bacteria and Haloarcula marismortui, an extremely halophilic aerobic mesophilic archaeon, are not significantly more than expected for their genome sizes (Fig. 3C). [SEP] Justify:

Output: The text corroborates the claim by discussing the mechanisms of horizontally transferred genes identified by the DarkHorse algorithm in bacteria. It highlights the significant number of potentially horizontally transferred genes in specific bacterial and archaeal pairs, which supports the idea that bacteria can acquire new traits through horizontal gene transfer (HGT). The reference to the comparisons of shared gene counts and the identification of such genes reinforces the role of HGT in bacterial adaptation and trait acquisition.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: A piece of opaque duct piping (24 cm in height with a diameter of 15 cm) fit completely around the inner compartment to block visual detection of external cues in the outer aquarium during the first segment of the trial. The trial began after a five minute acclimatization period, and lasted 35 minutes, divided into three segments. The first 15 minutes of the trial, the tadpole was filmed devoid of any cues/treatment to get an estimate of the individual's baseline activity. This allowed individual variation in activity to be statistically removed from the analysis. At the end of the first segment, 150 mL of one of the four treatments was added to the inner tadpole container (bringing the total volume within the container to 300 mL): (1) control (conditioned water was added), (2) parasite only (150 mL of water inoculated with 36 echinostome cercariae was added to give a treatment density of 36 cercariae per 300 mL), (3) fish only (150 mL of water from sunfish's home tank was added), (4) ‘fish+parasite’ (150 mL of water from the sunfish's home tank was inoculated with 36 cercariae and then added). This density of cercariae used was selected to reflect a moderate level of infection, and is within the range of infection intensities observed within wild caught animals, e. g. [21]. We used only simple predator kairomones (e. g. the “scent” of the predator alone) known to elicit antipredator behaviors in tadpoles [6]; note that diet cues were unattainable for the current study as experienced sunfish refuse to consume unpalatable bullfrog tadpoles [22]. As the treatment water was added, the opaque duct piping was removed exposing the tadpoles to all external visual cues. The second segment of the trial was a 5 minute (while filming) acclimatization period. In the third and final segment of the trial, tadpole post-treatment behavior was recorded for 15 minutes. At the end of the trial, the tadpole was removed to a separate container. The inner chamber was then emptied and wiped clean using 70% ethanol followed by a thorough wipe using dechlorinated water to remove any potential remaining cues prior to the next trial. All videos were watched and scored by one individual (DS) while blind to treatment. [SEP] Justify:

Output: The text contrasts the claim by describing a study involving tadpoles, which exhibit antipredator behaviors in response to predator kairomones. This indicates that at least some amphibians do have methods of defending themselves from predators, thereby rebutting the claim that they have no means of defense.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Codon usage bias and gene evolution in Juglandaceae plastomes The codon usage pattern of the Juglandaceae plastomes plays an important role in exploring its evolutionary process [45]. In our study, codon bias of Juglandaceae plastomes were investigated. The frequency of usage of multiple synonymous codons encoding the same amino acid is not equal, a phenomenon known as codon usage bias [46]. The relative synonymous codon usage (RSCU) can directly reflect the preference of codon usage [47]. So RSCU values of all selected plastomes were calculated. We found that the third base of most codons ends with A or U (Table S7a), this result is consistent with the results of studies such as Crataegus [48], Pisum [49], and Miscanthus [50], indicating that the third base in the plant plastomes may have similar usage patterns [51]. By constructing high and low expressed gene sets, codons with RSCU > 1 and ΔRSCU > 0. 08 were defined as optimal codons. Then, nine optimal codons of Juglandaceae plastomes were determined, all ending with A or U (Table S5d). In general, G and C (or A and T) are distributed proportionally at the third codon base, indicating that the codon usage bias of the species is affected by mutational pressure; if disproportionately distributed over the third base of a codon, it indicates that the codon usage bias is influenced by natural selection pressure [52]. Therefore, it was speculated that the codon bias in the plastid genome sequence of Juglandaceae is not only affected by base mutations, but also affected by natural selection pressure. Genes from Engelhardioideae, Juglandoideae and Rhoipteleoideae species were presented in different colors in ENC and PR2-plots (Fig. 7). There is no significant potential difference in the main driving forces of codon use bias among these three subfamily plants (Fig. 7; Table S7). We found a positive correlation between the codon preference index (CBI) and the optimal codon usage frequency (Fop), with the highest correlation coefficient of 0. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses the codon usage bias and gene evolution in Juglandaceae plastomes, which does not provide any insights or information related to artifacts or past cultures.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: In general, the bacteria that share unusually large numbers of genes with archaea (i. e. , after correction for genome size) are predominantly anaerobic and/or thermophilic (Fig. 5A). Bacteria isolated from hot springs, oil wells, sediments and activated sludge were over-represented in this set of bacteria (Fig. 5B). This result is remarkable considering that most of the bacterial genomes used in this study were from aerobic mesophiles (Fig. 5A). These trends are also true in the converse; i. e. , anaerobic and (hyper)thermophilic archaea are more likely to have large numbers of RBHs with bacteria (Fig. S6). In contrast, aerobic mesophilic archaea have a small number of RBHs with bacteria and form the fewest archaea-bacteria pairs enriched in RBHs (Fig. S6). Figure 5: Comparison of bacteria enriched in shared genes with archaea to the composition of the database. Pie charts comparing the bacterial database, excluding pathogens, to the bacteria that formed pairs enriched in shared genes (RBHs) with at least one archaeon. (A) Color coded with oxygen utilization and growth temperature of the bacteria (B) Color coded with the environment where the bacteria was isolated. Download full-size image DOI: 10. 7717/peerj. 3865/fig-5 To investigate more precisely which types of archaea and bacteria are more likely to share genes, we examined whether the archaea and bacteria in each enriched pair shared their growth conditions and habitats (Fig. 6). Indeed, in general, anaerobic bacteria share unusually large numbers of genes with anaerobic archaea, and (hyper)thermophilic bacteria share unusually large numbers of genes specifically with (hyper)thermophilic archaea (Fig. 6). One explanation of this result is that bacteria and archaea that live in similar environmental conditions are more likely to share genes with each other. However, this does not seem to apply to aerobic mesophilic bacteria. While all hyperthermophilic bacteria, 80% of thermophilic bacteria were enriched with at least one archaeal partner, and 56% of anaerobic bacteria were enriched in shared genes, Very few aerobic mesophilic bacteria were ever included in enriched pairs, even with aerobic mesophilic archaea (Fig. [SEP] Justify:

Output: The text corroborates the claim by discussing how bacteria share a large number of genes with archaea, particularly in specific environmental conditions. This sharing of genes is indicative of horizontal gene transfer, which is precisely how bacteria can acquire new traits. It also mentions that anaerobic and thermophilic bacteria specifically demonstrate this gene-sharing behavior with archaea, supporting the notion that horizontal gene transfer is a significant mechanism for trait acquisition among bacteria.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: Lithobates clamitans larvae also had more encysted metacercariae than L. catesbeianus, but the difference between fish present and fish absent treatments did not differ significantly for either L. clamitans or L. catesbeianus (based on model contrasts; Fig. 4). Download: PPTPowerPoint slidePNGlarger imageTIFForiginal imageFigure 4. Mean (± SE) number of encysted metacercariae (out of a potential 36 cercariae) for all three species in the parasite only and ‘fish+parasite’ treatments. The species by fish presence interaction was significant (negative binomial GLM analysis of deviance, species by fish; deviance = 206. 90, P = 0. 047). tadpoles were not dissected to check for potential parasite infection, however, in multiple subsequent parasitism experiments using the same amphibian and parasite species (unrelated to the current study), we have never found parasites in the control tadpoles (pers. obs. ) DiscussionOur behavioral results indicate that larvae of three Lithobates species respond differently to the trade-off imposed by the simultaneous presence of both a predator and parasites. An anti-predator response dominates behavior of L. sylvaticus in the presence of both fish and parasites, and anti-parasite behavior dominates the response of L. catesbeianus in the presence of both fish and parasites. The behavior of L. clamitans in the combined fish and parasite treatment was also biased toward anti-parasite behavior, but to a lesser extent than in L. catesbeianus. Larvae of all species increased time active in the presence of parasites alone, clearly demonstrating that tadpoles respond to the presence of parasites with increased activity. Further, this increased activity is effective in reducing parasitism, as indicated by the significant difference in encysted echinostomes between the parasite only versus the ‘fish+parasite’ treatment for L. sylvaticus (the species with the most dramatic change in time active between the parasite only and the fish+parasite treatments). Koprivnikar et al. [16] also observed a relationship between activity and parasitism in L. [SEP] Justify:

Output: The text contrasts the claim by describing the behavioral responses of Lithobates species to the presence of both predators and parasites. Specifically, it notes that an 'anti-predator response dominates behavior of L. sylvaticus in the presence of both fish and parasites,' indicating that these amphibians have methods of defending themselves from predators. Furthermore, the increased activity in response to parasites implies that tadpoles exhibit behavior that can potentially reduce predation risk.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: 97, indicating that the codon usage pattern in the plastomes of Juglandaceae may be determined by the optimal codon usage frequency during evolution [45]. In the Juglandaceae and two subfamilies (Juglandoideae, Engelhardioideae), 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], so we inferred that the content of the third base of synonymous codons in Juglandaceae and two subfamilies (Juglandoideae, Engelhardioideae) 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). In the Rhoipteleoideae subfamily, C3s, G3s, and GC3s are positively correlated with gene expression, while T3s and A3s are negatively correlated with gene expression (Fig. S5). There are 50 protein-coding genes with lengths longer than 300 bp in the plastomes of Juglandaceae. The ENC values of these screened gene coding sequences range from 35. 71 to 60. 60. According to the ENC values ranging from 20 (completely biased) to 61 (unbiased) [53], and when the ENC value is less than 35, the codon usage of the gene or genome has a strong bias [54]. Based on these two characteristics, we found that the codon usage bias of protein-coding genes in Juglandaceae plastids was weak. There were 2051 ENC frequency ratios between − 0. 1 and 0. 1 (Table S7f), which were close to the expected ENC value, indicating that the difference between the expected ENC value and the actual values of most genes are small. The results showed that the content of bases at the third position of synonymous codons was closely related to gene expression. The GC content of the third base of codons (GC3s) is considered to be most likely to directly reflect codon usage patterns [55] and may be an important factor leading to codon usage bias. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses codon usage patterns and gene expression in the Juglandaceae family without any mention of artifacts or insights into past cultures. The content primarily focuses on scientific data related to genetics rather than anthropological or cultural implications.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: 001 Low vs significant pH (2 way w/Temp) Not significant with 16S Matrix 0. 176 0. 000 DOI: 10. 7717/peerj. 3865/table-1 Like the number of reciprocal best hits, the number of potentially transferred genes is highest among anaerobic or thermophilic bacteria and anaerobic or thermophilic archaea (Fig. 4 and Fig. S5). sp. BAV1, 12–31% of total shared genes were horizontally transferred, and this was fairly typical for bacteria enriched in shared genes. The numbers of transferred genes were larger than the residual from the upper confidence interval for shared genes, but these two numbers are not necessarily comparable. However, it does seem likely that a large proportion of the extra shared genes in enriched archaea-bacteria pairs (i. e. , those identified by our correction for genome size) were horizontally transferred. Figure 7: Examination of horizontal gene transfer in individual bacteria. Bacteria that form pairs with >3 archaea for either the number of residual reciprocal best hits (RBH) or potentially horizontally transferred genes, as determined by DarkHorse. The color coded bar graphs represent the number of archaea with which that bacterium forms enriched pairs (similar to Fig. 6). Bacterial names (left) are also color coded by bacterial oxygen utilization and growth temperature as in legend. Circles next to bacterial names indicate bacterial isolation environment. The column of numbers indicates the average number of horizontally transferred genes from archaea to bacteria for each category of archaea in the order aerobic thermophilic, anaerobic thermophilic, anaerobic mesophilic, and aerobic mesophilic archaea. The average number of HGT genes from archaea to bacteria for the entire dataset is four. Download full-size image DOI: 10. 7717/peerj. 3865/fig-7 The DarkHorse results on horizontal gene transfer can be evaluated to determine the direction of transfer (i. e. , from bacteria to archaea or from archaea to bacteria). Most documented cases of HGT between bacteria and archaea are predominantly unidirectional from bacteria to archaea (Wiezer & Merkl, 2005; Kanhere & Vingron, 2009; Nelson-Sathi et al. , 2015). [SEP] Justify:

Output: The text corroborates the claim by detailing how horizontal gene transfer (HGT) occurs among bacteria and archaea. It mentions that a significant portion of shared genes between bacteria and archaea are horizontally transferred, indicating that bacteria can acquire new traits through this process. Specifically, it discusses the average number of horizontally transferred genes from archaea to bacteria and highlights the prevalence of HGT as a means of gene acquisition, thereby supporting the claim.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: clamitans, with tadpoles more likely to be infected when they were less active (the number of cysts per tadpole did not differ, but tadpoles were exposed to only five cercariae). Similarly, Pseudacris regilla anesthetized to prevent behavioral response have a greater infection prevalence and intensity from Echinostoma than conspecifics not anesthetized [19]. Activity level cannot fully explain differences in parasite intensity in our study: all species were equally active in the parasite only treatment, yet L. sylvaticus had greater numbers of encysted parasites than either L. clamitans or L. catesbeianus (Fig. 4). Fewer L. sylvaticus tadpoles displayed body twist behavior than either L. clamitans or L. catesbeianus. Thus, one possible explanation for difference in parasite intensity among species is that body twists are an especially good behavioral mechanism for dislodging echinostome cercariae. Unfortunately, the methodology of the current study did not allow us to correlate an individual's behavior with its subsequent parasite numbers. Future studies doing this will be useful in clarifying the role of these behaviors in avoiding/dislodging potential parasites. That said, it seems unlikely that this one behavioral difference is sufficient to explain the increased number of successful parasites in L. sylvaticus and it does not explain observed differences in parasite intensity between L. clamitans and L. catesbeianus. As with differences in predators among habitat types, it is possible that the three species tested in this study experience different levels of parasite exposure in the wild. While trematode parasites are common and prevalent in amphibian populations [16], [34], temporary pond breeders such as L. sylvaticus may encounter cercariae of echinostomes less frequently or for a shorter period of time than either L. clamitans or L. catesbeianus (although L. sylvaticus have been observed with Echinostoma cysts in the field [35]). For example, L. sylvaticus metamorphose within a single season where both L. clamitans and L. catesbeianus typically overwinter as tadpoles [36], spending an additional summer in the pond, which in turns exposes them to trematode parasites for a much longer period than L. [SEP] Justify:

Output: The text contrasts the claim by discussing how certain amphibians, specifically L. sylvaticus, display body twist behavior as a mechanism to dislodge parasites, which may imply that amphibians do have behavioral strategies that could be seen as defensive actions. The mention of differences in predator exposure also suggests that amphibians have varying strategies and behaviors in response to threats, contradicting the claim that they have no methods of defense.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: The scatter plot was drawn with ENC as the ordinate and GC3s as the abscissa to explore the main features of codon usage (Fig. 7). When the scatter points are on or near the standard curve, it indicates that the codon preference is affected by mutational pressure, and vice versa, it indicates that the codon usage preference is affected by factors such as natural selection [56]. It was found that most of the scatter points were located on or near the curve (Fig. 7), indicating that the mutation had a greater effect on codon bias. Further ENC-plot analysis showed that the ENC values of most genes were close to the expected value (Fig. 7A), suggesting that the codon usage biases of these genes were related to GC3, and mutation was the main factor influencing factor. In addition, some genes (rpl16, rps18, and rps14) were much lower than the expected curve (Fig. 7), which also confirmed the influence of natural selection on codon p97. 69 Mya (95% HPD: 95. 49–100. 58 Mya) using a older fossil time node from a fossil plant Budvaricarpus serialis (ca. 85 Mya) [72] [73]. The three subfamilies Rhoipteleoideae, Engelhardioideae, and Juglandoideae, successively differentiated at 89. 28 Mya (95% HPD: 85. 61–92. 96 Mya) and 73. 59 Mya (95% HPD: 69. 01–78. 13 Mya) (Fig. 9). subfamily differentiated approximately between 69. 01 and 78. 13 Mya, from Cretaceous to Paleogene. [74, 75] provides a reasonable explanation for the origin and diversity of the Juglandoideae subfamily, that is during the warm Paleocene and Eocene periods, species of the Juglandoideae subfamily formed and rapidly diversified, spreading from to Europe and Asia through the and the Bridge [76]. However, the global cooling that occurred after the extreme heat period of the led to the extinction of most species [77–79]. and Platycarya were endemic to East Asia, while Pterocarya were mainly distributed in the Caucasus and regions of southern Russia. [SEP] Justify:

Output: The text is irrelevant to the claim as it focuses on genetic analysis, codon usage, and the evolutionary history of certain plant subfamilies rather than discussing artifacts or their significance to understanding past cultures. There is no mention or discussion of artifacts or insights into daily lives in the provided text.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: The number of transferred genes from bacteria to archaea may be five-fold larger than the number of genes transferred from archaea to bacteria (Nelson-Sathi et al. , 2015). Our results agree with this trend for “normal” archaea-bacteria pairs (i. e. , those that are not enriched in shared genes); these pairs generally have more genes transferred from bacteria to archaea (Fig. 4 column 3; Table S4). However, of the 58 bacterial genomes that form pairs for enriched numbers of shared genes, over half had 11 or more genes horizontally transferred from archaea to bacteria (Fig. 7), whereas the mean number of archaea to bacteria transfers for all genomes is only 4 ± 7. Anaerobic and (hyper)thermophilic bacteria have more transferred genes from anaerobic and (hyper)thermophilic archaea, respectively, than from aerobic or mesophilic archaea (Fig. 7). Some bacteria, such as Dictyoglomus and Dehalococcoides, have 30–50 horizontally transferred genes from archaea (Fig. 7). These results suggest that the unusually large numbers of shared genes in our enriched archaea-bacteria pairs is primarily due to an unusually large number of gene transfers from archaea to bacteria in anaerobic and (hyper)thermophilic conditions. Examination of halophily Given that the numbers of shared genes are strongly associated with bacterial growth temperature and oxygen utilization, the lack of any significant correlation with halophily is surprising (Table 1) though consistent with results from Rhodes et al. (2011). There appears to be no difference in the numbers of shared genes between bacteria and archaea for non-halophilic and moderately halophilic bacteria. Of the six extremely halophilic bacteria, only two, Salinobacter ruber and Chromohalobacter salexigens, were ever enriched in RBHs. Salinibacter ruber, which is known to share genes with haloarchaea, including rhodopsins and a hypersalinity island (Mongodin et al. , 2005), was enriched in shared genes with each of the six extremely halophilic archaea. Salinibacter also possessed many horizontally transferred genes from archaea (Fig. 7). [SEP] Justify:

Output: The text corroborates the claim by discussing multiple instances of horizontal gene transfer occurring between archaea and bacteria. It details how certain bacteria, such as Dictyoglomus and Dehalococcoides, have acquired a significant number of horizontally transferred genes from archaea, supporting the idea that horizontal gene transfer enables bacteria to acquire new traits.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: sylvaticus tadpoles. In addition, the first intermediate host of E. trivolvis is the snail P. trivolvis and this species is most often found in permanent pond settings, namely well vegetated lentic or still waters and farm ponds, dams, lakes [37]. As L. sylvaticus often inhabit temporary ponds that can dry by the end of the season, these ponds are generally not suitable habitats for P. trivolvis snails. However, there are ponds that are more permanent in that they do not dry regularly, yet lack major vertebrate predators such as fish; these ponds would be suitable habitats for both P. trivolvis and breeding L. sylvaticus (in fact, our L. sylvaticus eggs were collected from a large permanent lake that lacks fish predators). In ponds that dry often, other species of snails (e. g. Pseudosuccinea columella) that can undergo aestivation during dry periods, persist along with other macroparasites that also use larval amphibians as a secondary host (e. g. Telorchis spp. ) [38]. Further studies of parasite distributions among ponds that vary in permanence will allow us to better relate putative antiparasite behaviors to ecologically relevant conditions. We demonstrate here that the presence of multiple enemies (parasites and predators) in an environment lead to non-additive behavioral responses in tadpoles that are species-specific. An important caveat to this interpretation of species-specific effects is that we had limited genetic diversity of L. catesbeianus and L. clamitans tadpoles (our L. catesbeianus individuals were from a single egg mass). While this is far from ideal, the egg mass was collected at random (through extensive blind dip-netting in a large lake) and we have no reason to believe that these individuals were not representative of the species response. Nonetheless, within species variation in response to predators and parasites is known to occur, at least in L. sylvaticus [30]. Thus future studies replicating the observed differences among species and expanding the species considered are necessary. In addition, future studies should also include other potentially important variables such as differences in temperature preference among species, differences in oxygen concentrations within the different habitats and habitat complexity, as these factors may influences susceptibility to both predators and parasites. [SEP] Justify:

Output: The text contrasts the claim by discussing how tadpoles exhibit non-additive behavioral responses to the presence of multiple enemies, including predators and parasites. It highlights that there are species-specific behavioral responses to predators, indicating that amphibians, specifically L. sylvaticus, have methods to deal with predation. This suggests amphibians do have means of defending themselves against predators, countering the claim.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Carya and Juglans have a wide distribution range in Eurasia, possibly due to their nutty fruit morphology, which facilitates animal transportation and transmission [3]. According to our results, the divergence time of Carya and Juglans was about 64. 98 Mya, of Juglans and Pterocarya was about 46. 29 Mya, of Pterocarya and Cyclocarya was about 54. 10 Mya. Therefore, we inferred that differentiation events within the Juglandoideae subfamily occurred a long time ago and had undergone a long evolutionary process [21, 66]. The divergence time of the two clades in the Engelhardioideae subfamily was approximately between 27. 64 and 46. 11 Mya, mainly occurring from the to the Middle Oligocene. The earliest fossil record of the fruit of Engelhardia existed in and the oldest Alatonucula ignis fossil had been found in the early Eocene strata of Argentina [65]. At the same time, a fossil was found in the Miocene strata of Alaska, USA (Palaeocarya olsoni) [70]. This means that these taxonomic groups were widely present in parts of the Northern and during the Eocene. Perhaps due to the high temperatures in the Paleogene, the species of Engelhardia were widely distributed in high latitude areas. Based on the discovery of the earliest fruit fossil of Palaeocarya in China in the strata of (Palaeocarya sp. ) [80], it indicates that Engelhardia plants began to occupy tropical Asia in the late Eocene, while species diversity emerged in the Oligocene Miocene. In short, our study accurately estimated the divergence time of Juglandaceae species using 80 coding sequences (CDs) from plastomes. And we found that Juglandaceae species had a complex evolutionary history and species diversity, which may be influenced by geographical changes, climate changes, and animal coevolution during the evolutionary process. ConclusionThis study analyzed characteristics of the plastid genome of newly sequenced species of 8 Engelhardia species, and clarified that the basic structure of the plastid genome was a typical tetrad structure. Three mutation hotspot regions were found and they can be used as potential molecular markers for infering phylogenetic analysis and species identification. [SEP] Justify:

Output: The text does not address the claim about artifacts providing insights into past cultures. Instead, it discusses the evolutionary history and taxonomic classifications of various plant species, as well as their divergence times and fossil records. There is no mention of artifacts or daily lives of cultures, making the text irrelevant to the claim.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: Salinibacter was isolated from a salt cistern, which is the saltiest habitat known to harbor bacteria (Mongodin et al. , 2005). None of the other extremely halophilic bacteria in this dataset reach the ultra-extreme halophily of Salinobacter (Hirschler-Rea, 2003; Hou et al. , 2004; Mongodin et al. , 2005; Auman et al. , 2006; Hoeft et al. , 2007). is an exception among the six halophilic bacteria examined here in its extensive sharing and transferring of genes with archaea, and this may be related to its extreme halophily. We do not deny that halophilic archaea have been changed by horizontal gene transfer with bacteria. However, the ancient transfer of 1,000 bacterial genes that allowed the class Haloarchaea to form from methanogens (Nelson-Sathi et al. , 2012) would not be marked as transferred in our scheme because the genes are present in several genera. Additionally these genes don’t appear to be shared specifically with other modern sequenced halophilic bacteria. Correlation with genome %GC Along with oxygen utilization and growth temperature range, bacterial genome %GC content was also a significant factor correlated with the number of shared genes (Table 1). As has been noted previously (Naya et al. , 2002; Wu et al. , 2012), in our dataset aerobic bacterial genomes have a significantly higher %GC (59%) than anaerobic bacterial genomes (45%; p < 0. 001) but GC content does not correlate with oxygen utilization in archaea. Similar to Hurst & Merchant (2001), GC content does not correlate between temperature groups in either archaea or bacteria in our dataset. To verify that %GC is not confounding the effect described above for anaerobes and (hyper)thermophiles, we repeated our analyses after correcting for both genome size and genome %GC by multiple linear regression (Fig. S4). The magnitude of the %GC correction (average of 2. 6 per 10% GC change) was much smaller than that for the original genome size correction (average 45 per 1,000 genes). Interestingly, a relationship between GC content and reciprocal blast hits was only significant for aerobic archaea (p < 0. 01). [SEP] Justify:

Output: The text corroborates the claim by providing evidence of horizontal gene transfer among Salinibacter and archaea. It specifically mentions that Salinibacter engages in extensive sharing and transferring of genes with archaea, indicating that horizontal gene transfer is indeed a mechanism through which bacteria can acquire new traits. Furthermore, it acknowledges that halophilic archaea have been altered by horizontal gene transfer with bacteria, directly supporting the claim.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: Regardless, our data add to a growing body of evidence that suggests parasites and pathogens in animal communities can have trait-mediated indirect effects that influence predator-prey interactions. Contrary behavioral responses to parasites and predators have been observed in damselfly larvae [20] and Daphnia [39], as well as tadpoles [27], [40], [41]. While the potential for non-additive and trait-mediated interactive effects among predators that share prey within a community is well-recognized, consideration of parasites within this context has been neglected until recently [10]. ConclusionsIn this study we demonstrate three important and novel results regarding tadpoles, their predators and their parasites: i) in the presence of free-swimming trematode cercariae, tadpoles increase general activity and some specific behaviors such as body twisting; ii) this behavioral response to parasites corresponds to decreased parasite encystment success; iii) species respond differentially to the trade-off imposed by the presence of both parasites and fish predators as predicted based on the presence of alternative (non-behavioral) antipredator traits. Our results add to a growing body of evidence that as well as the potential for interactions among the direct effects of predators and parasites, substantial indirect interactive effects may occur through trait-mediated effects, particularly behavioral responses of potential prey/hosts to the presence of predators and parasites. Further, these effects are likely to be species-specific, dependent on the suite of traits species possess that affect predation and parasitism risk. Recognition of the increased complexity of interactions among species within a community places greater urgency on our ability to quantify and understand such interactions if we are to predict the effects of the changes in biodiversity currently affecting communities at unprecedented rates [42]. 1. (1990) Behavioral decisions made under the risk of predation - a review and prospectus. Zool 68: 619–640. View 2. Taylor RJ (1984) Predation. New York, U. S. A: Chapman and Hall. 3. (1979) Suspension feeding dynamics of anuran larvae related to their functional morphology. Oecologia 39: 259–272. View 4. (1995) Interaction between food availability and predation mortality mediated by adaptive behavior. Ecology 76: 2230–2234 View 5. Lawler SP (1989) Behavioral responses to predators and predation risk in four species of larval anurans. [SEP] Justify:

Output: The text contrasts the claim by detailing how tadpoles, a type of amphibian, exhibit behavioral responses to the presence of predators and parasites, such as increasing general activity and body twisting. This indicates that amphibians do have methods to defend themselves, contrary to the claim that they lack any defensive strategies.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: InDels may be an important driving factor for the plastome evolution of Juglandoideae and Engelhardioideae. Natural selection and mutation jointly affected the codon usage patterns of Juglandaceae and three subfamilies, with mutation pressure playing a major role. Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. Divergence time analysis revealed that Engelhardia originated in the later Cretaceous and diversified in the later Eocene, and Juglandaceae originated in the and differentiated in Middle Cretaceous. Overall, this study demonstrated that the plastome sequences displayed variable information to resolve phylogenetic relationships and were helpful to understand how species adapts to diverse ecological habitats. Materials and methods Plant materials and DNA extraction In this work, a total of 13 individuals from all currently recognized 8 species of Engelhardia (E. anminiana, E. fenzelii, E. hainanensis, E. roxburghiana, E. serrata, E. spicata, E. spicata var. rigida, and E. villosa) and one outgroup species Rhoiptelea chiliantha were collected in the tropical and subtropical Asia. The materials were identified by Yong-Hua Zhang, Hong-. The fresh leaves from each accession were dried with silica gel for further DNA extraction. Total high-quality genomic DNA was extracted from all plant materials using Plant DN(Biotechnology Co. , Ltd, Hangzhou, China). The detailed information of taxon, voucher number, collector and GenBank accession number are listed in Table 1. DNA resequencing, plastomes assembly and gene annotation High-quality genomic DNA from each sample was used for the whole genome sequencing (WGS) to obtain paired-end 100 bp raw reads on the -500 platform (BGI, Shenzhen, China) according to the manufacturers’procedures. The quality of raw reads was controlled by removing the Phred score lower than 30, remaining the high-quality sequences for genome assembly using the GetOrganelle software [81]. The command lines used for the assembly were as follows: get_organelle_reads. py -1 forward. fq -2 reverse. [SEP] Justify:

Output: The text is irrelevant to the claim. It discusses genetic research on the plastome evolution of specific plant families, including technical details about DNA extraction and sequencing. It does not provide any insights into past cultures or artifacts related to them.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: A two-way of the secondary residuals indicated that oxygen utilization and growth temperature of the bacteria were still significant factors affecting numbers of RBHs (aerobic vs. anaerobic R = 0. 382 p = 0. 001; mesophilic vs. hyperthermophilic R = 0. 676p = 0. 001). address the question of whether bacteria and archaea from the same habitats are more likely to engage in HGT, we categorized the DarkHorse and RBH results by the environment from which the archaea and bacteria were isolated. Habitats with similar temperature and oxygen characteristics, such as terrestrial hot springs and marine hydrothermal vents, have similar numbers of horizontally transferred genes and RBHs between bacteria and archaea (Fig. 8). A similar correspondence was observed with animal guts and sediments, both of which harbor a high proportion of anaerobic organisms involved in the degradation of complex organic matter (Fig. S7). These findings suggest that metabolic and physiological similarities could be more important in determining successful gene transfers between archaea and bacteria than co-habitation. However, our database does not include bacteria and archaea isolated from exactly the same area, which would be needed to examine this question more thoroughly. Figure 8: Comparison of transferred and shared genes with habitat. Comparison of transferred (A) and shared (B) genes with habitat. Particularly, we compare genes in hotsprings and hydrothermal vent bacteria to hotsprings and hydrothermal vent archaea. HGT stands for horizontally transferred genes, and RBH stands for reciprocal best hits or shared genes. Download full-size image DOI: 10. 7717/peerj. 3865/fig-8 Our findings do suggest that HGT is more common in some habitats than others. Oil wells, hot springs, and sediments are environments where bacteria and archaea share unusually large numbers of genes (Fig. 5B). 30% of bacteria with HGT genes >2 standard deviations above the mean were from hot springs, 32% were from sediments and 20% were from soil (Fig. 7). Thermophiles employ various mechanisms to mitigate DNA degradation at high temperatures, so thermophile-derived DNA may be more likely to persist both inside and outside of cells. [SEP] Justify:

Output: The text corroborates the claim by discussing examples of horizontal gene transfer (HGT) between bacteria and archaea across various habitats. It specifically states that in environments like hot springs and hydrothermal vents, bacteria are shown to share a significant number of horizontally transferred genes, suggesting that HGT is an important mechanism for bacteria to acquire new traits based on the environmental characteristics.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: 38: 1039–1047. View 6. Richardson JML (2001) A comparative study of activity levels in larval anurans and response to the presence of different predators. 12: 51–58. View 7. Liem KF (1961) On the taxonomic status of the granular patches of the Javanese frog Rana chalconota Schlegel. Herpetologica 17: 69–71. View 8. Relyea RA (2001) The relationship between predation risk and antipredator responses in larval anurans. Ecology 82: 541–554. View 9. (1998) Selection for phenotypic plasticity in Rana sylvatica tadpoles. 65: 301–328. View 10. (2008) Parasites as predators: unifying natural enemy ecology. Evol 23: 610–618 View 11. (2008) Emerging helminthiases in amphibians: lessons from Ribeiroia and Echinostoma. In: Fried B, Toledo R, editors. of Echinostomes. Berlin, Germany: Springer. 12. Huffman JE, (1990) Echinostoma and Echinostomiasis. 29: 215–269. View 13. Prudhoe S, Bray RA (1982) Platyhelminth parasites of the Amphibia. Oxford, U. K: Press. 14. (1997) Experimental infection of Rana pipiens tadpoles with Echinostoma trivolvis cercariae. 83: 666–669. View 15. (2009) The role of trematode parasites in larval anuran communities: an aquatic ecologist's guide to the major players. Oecologia 161: 371–385. View 16. (2006) On the efficacy of anti-parasite behaviour: a case study of tadpole susceptibility to cercariae of Echinostoma trivolvis. Zool 84: 1623–1629. View 17. (2009) Parasites, info-disruption, and the ecology of fear. Oecologia 159: 447–454 View 18. (2004) On the behavioural response of Rana and Bufo tadpoles to echinostomatoid cercariae: implications to synergistic factors influencing trematode infections in anurans. [SEP] Justify:

Output: The text contrasts the claim by presenting various studies indicating that amphibians, particularly larval anurans, demonstrate antipredator responses to the presence of predators. For instance, Relyea (2001) discusses the relationship between predation risk and these responses, which implies that amphibians employ strategies to defend themselves against predators, directly contradicting the claim that they lack any method of defense.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: fq -o plastome_output -R 15 -k 21,45,65,85,105 -F plant_cp. All targeted plastomes sequences were concatenated and manually edited with 2021 software ( using the plastome sequences of Carya sinensis (MN892516) and Rhoiptelea chiliantha (MT701585) as the reference genomes. At the same time, the 2 web server ( was used to predict the types and structures of all the protein-coding and non-coding genes in the plastomes. The final plastomes annotation was determined by comparing the results of 2021 and 2. Finally, CPGView [82] were used to visualize the plastome map. The 13 newly generated complete plastome sequences were deposited in GeneBank (Accession numbers were listed in Table 1). Plastomes of 43 other species were downloaded from repository and re-annotated using the earlier method, the GenBank accession numbers are shown in Table S1. Comparative analysis of plastome structure features We used these newly-sequenced Engelhardia individuals to study the genomic variation in Engelhardia. Two methods were used for comparative genomic analysis: (1) The comparison of the plastomes sequence identity was using MAVUE and mVISTA [83]. Sequence rearrangement detection was performed on 13 plastomes using the Mauve alignment plugin in 2021 software, and 13 sequences were aligned using the LAGAN model in the online software mVISTA. (2) The comparison of the expansion and contraction of IR regions was presented. The IR boundary regions were visualized by using the online website IRScope ( Repeat sequences detection The genome of organisms, especially higher organisms, contains a large number of repeat sequences, which can be divided into dispersed repeat sequence (DRS) and tandem repeat sequence [84] according to their distribution patterns in the genome. First, the DRS in the plastomes of 8 Engelhardia species were predicted by the REPuter software [85]. The forward, reverse, palindromic and complement repeat sequences were identified using the following parameters: length of repeat unit ≥ 30 bp, sequence consistency ≥ 90% (Hamming distance = 3). [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses a technical methodology for plastome analysis and does not mention artifacts or insights into past cultures. It focuses instead on genomic data and comparative analysis of plant species, which does not relate to the claim about providing insights into daily lives of historical cultures.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: This biochemical characteristic of thermophiles has been previously suggested as a possible cause for the greater prevalence of HGT events between thermophiles compared to halophiles (Rhodes et al. , 2011). Furthermore, oil wells and hot springs are typically dominated by biofilm communities (Blenkinsopp & Costerton, 1991; Meyer-Dombard et al. , 2011; Marks et al. , 2012), which are known to facilitate HGT due to the high density and close physical proximity of metabolically active cells (Molin & Tolker-Nielsen, 2003; Aminov, 2011). Sediments and soil also have a high density of microbial cells (Christensen, Hansen & Sørensen, 1999; Schippers et al. , 2012). Additionally, viral abundance and production in sediments is high compared to the water column (Danovaro et al. , 2008), and more than half of the DNA in sediments is extracellular (Dell’Anno & Danovaro, 2005). Therefore, all of these factors (cell density, viral abundance, and extracellular DNA) may promote HGT in sediments. Functional characterization of shared and transferred genes To gain more insight into the types of genes that may be shared more frequently between anaerobic and (hyper)thermophilic organisms, we examined the shared genes (RBHs) by functional category using the COG database (Tatusov et al. , 2003) (Table S5). Some COG categories are more likely than others to contain genes shared between bacteria and archaea. Specifically, the categories Energy Production, Translation, Nucleotide Metabolism, and contain a higher proportion of archaea-bacteria RBHs than that found in the total set of genes in all genomes (Fig. 9). Curiously, HGTs identified by DarkHorse are not enriched in these same categories; instead, they are more abundant in Transport and Metabolism (such as metal or sodium transporters), and Conversion, and Transport and Metabolism (Fig. 9B). [SEP] Justify:

Output: The text corroborates the claim by discussing horizontal gene transfer (HGT) in the context of thermophiles and the factors that facilitate HGT, such as high cell density, viral abundance, and extracellular DNA. It details how different environmental conditions, specifically those in sediments and biofilm communities, enhance the likelihood of HGT occurring among bacteria, thus supporting the idea that HGT is a mechanism for bacteria to acquire new traits.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: Figures AbstractThe acquisition of sensory information by animals is central to species interactions. In aquatic environments, most taxa use chemical cues to assess predation risk and other key ecological factors. A number of laboratory studies suggest that anthropogenic pollutants can disrupt chemoreception, even when at low, non-toxic concentrations, but there are few tests of whether real-world variation in water quality affects chemoreception. Here we investigate whether chemosensory perception of predators by the gray treefrog, Hyla versicolor, depends on water quality. We evaluated the anti-predator response of anuran tadpoles housed in water collected from three sites that represent strong contrasts in the concentration and types of dissolved solids: de-chlorinated tap water, water from an impaired stream, and treated wastewater effluent. Behavioral assays were conducted in laboratory aquaria. Chemical cues associated with predation were generated by feeding tadpoles to dragonfly predators held in containers, and then transferring aliquots of water from dragonfly containers to experimental aquaria. Tadpoles housed in tap water responded to predator cues with an activity reduction of 49%. Tadpoles housed in stream water and wastewater effluent responded to predator cues by reducing activity by 29% and 24% respectively. The results of factorial ANOVA support the hypothesis that the response to predator cues depended on water type. These results show that alteration of the chemical environment can mediate chemical perception of predators in aquatic ecosystems. Because most aquatic species rely on chemoreception to gather information on the location of food and predators, any impairment of sensory perception likely has important ecological consequences. Citation: (2015) of Predators by Depends on Water Quality. 10(6): e0131516. Peter P. : February 18, 2015; Accepted: June 3, 2015; Published: June 26, 2015Copyright: © 2015 Troyer, Turner. This is an open access 4939. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. IntroductionSensory information plays a central but often unappreciated role in shaping species interactions. [SEP] Justify:

Output: The text contrasts the claim by demonstrating that gray treefrog tadpoles possess behavioral responses to predatory cues, reducing their activity when exposed to these cues. This indicates that amphibians, such as tadpoles, have methods of detecting predators and thereby defending themselves, contradicting the assertion that they have no means of self-defense.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Then, the TRS in the plastomes were predicted using the Finder (TRF) web server ( Finally, the MISA software was used to identify simple sequence repeats (SSR), setting the minimum repetition threshold values for mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide were set to 10, 5, 4, 3, 3, 3, respectively. Analysis of nucleotide polymorphism and mutation sites We analysed nucleotide polymorphisms based on the Pi values of Carya, Engelhardia, and Juglans, respectively. The plastomes were aligned using mafft alignment with default settings in 2021. of protein-coding genes, noncoding genes, and the intergenic regions extracted from the plastome was calculated using DnaSP v6. 0 [86] to show the nucleotide diversity at genus level. In order to eliminate interference from different individuals of the same species, we only chosen E. hainanensis_HN01, E. fenzelii_TTD01 and E. roxburghiana_BPZ11 accessions on behalf of E. hainanensis, E. fenzelii, and E. roxburghiana, respectively. The parameters were set as: window length = 600 bp, step size = 200 bp. After that, the corresponding loci were located and counted in 2021 software, and sequence fragments with Pi values greater than 0. 01 were used as candidate high variation regions. In order to conduct comprehensive comparison of genomic variation of Carya, Engelhardia, and Juglans plastomes, we calculated their total number, length, and percentage of SNVs and insertion and deletions (InDels) sites located in gene intervals, exons, introns, and RNA genes. species, we only kept one individual from the same species to conduct nucleotide polymorphisms analysis. To draw density bar graphs of SNVs, InDels data, we used the plugin in TBtools, and the detection parameters were set as: the number of threads (CPU) to 2, the genome sequence divergence standard (Diff) to OneIn Thousand, VarRange from 0 to 1000000. Carya, Engelhardia, and Juglans were aligned with R. chiliantha, which was selected as the reference sequence, then variation site information was outputted. [SEP] Justify:

Output: The text does not relate to the claim regarding artifacts and their insights into past cultures. Instead, it discusses genomic analysis processes and methodologies without mentioning artifacts, cultures, or any related insights.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: Consistent with previous findings that transferred transporters were enriched in Methanosarcina genomes (Garushyants, Kazanov & Gelfand, 2015), transporters were especially enriched in HGTs in our dataset: 15% of HGTs involved transporters of some kind compared to 5% in the whole dataset of all genomes. Indeed, transporters can be expected to confer immediate benefits to a cell after horizontal transfer. Figure 9: COG categories of genes shared between archaea and bacteria. (A) COG categories of all genes in all genomes, (B) all genes shared between bacteria and archaea as measured by RBHs, and (C) all genes identified as HGTs by DarkHorse. (D) Boxplot comparing COG cateogories that are enriched in HGTs. (E) Boxplot comparing COGs that are enriched in RBHs. In the boxplots, the lines represent the mean, points represent outliers, the edges of the box are the 25th and 75th percentiles and the whiskers represent the 90th percentile. Values in the boxplots are normalized by the appropriate total numbers of genes. Download full-size image DOI: 10. 7717/peerj. 3865/fig-9 Interestingly, archaea and bacteria share many genes in the Translation category, but these genes are not horizontally transferred (Fig. 9C). This is consistent with translation proteins being highly conserved between archaea and bacteria (Koonin et al. , 2012) and is likely an example of genes shared from vertical descent. and Metabolism genes are also frequently shared by archaea and bacteria but not horizontally transferred (Fig. 9C). Notably, Transcription and genes do not seem to be shared between bacteria and archaea (Fig. 9). The lack of shared genes in these categories is not surprising (Cordero & Hogeweg, 2009), considering that archaea and bacteria employ completely different transcription machinery (Jun et al. , 2011) and signal transduction pathways (Ulrich, Koonin & Zhulin, 2005). The abundance of shared genes in each COG category was normalized for genome size using the empirical fit log–logistic function (Table S6). As with the total dataset, temperature, oxygen utilization and GC content were all significantly correlated with the number of shared genes in many COG categories (Table 2). [SEP] Justify:

Output: The text supports the claim by discussing horizontal gene transfers (HGTs) and their role in enriching Methanosarcina genomes with transporters. It indicates that transporters can confer immediate benefits to a cell following horizontal transfer, directly linking HGTs to the acquisition of new traits in bacteria.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: Foragers require accurate data regarding the location and identity of prey in order to successfully acquire food, and prey require data regarding the location, identity, and abundance of predators in order to successfully employ anti-predator defenses. The outcome of these important processes depends on the quality and quantity of sensory information [1]. Thus, species interactions emerge from information conveyed among individuals, and species embedded in an ecological community are connected by an “information web” just as they are interconnected by a food web [2]. In aquatic ecosystems, reception of chemical cues that provide information regarding predators, food, and potential mates is likely the predominant sensory modality [3–4]. The conveyance of these chemical cues, often referred to as infochemicals [5], plays an important role in the ecology of many aquatic communities. For example, by using odors in the water, the freshwater snail Physa acuta can assess the proximity of predators in its immediate environment, the history of predator presence, the species-level identity of the predators, and even discern the recent diet of potential predators [6–8]. Based on this detailed sensory information, P. acuta alters its behavior, morphology, and life-history in an adaptive manner. These shifts in phenotype, in turn, affect the snail’s resources, its competitors, and its predators [9]. In a similar manner, many larval anurans respond to predators with changes in activity, morphology, and life history, and these shifts have a strong influence on competition among anuran species [10–11]. In this way, species affect each other’s population growth rates not just by consuming and being consumed, but also by inducing shifts in the phenotypes of species with which they interact. Trait shifts that propagate through the food web and alter the strength of species interactions are called trait-mediated indirect effects. An accumulating body of evidence shows that trait-mediated indirect effects can play an important role in organizing communities [12]. Research also shows that for aquatic communities, chemical cues are often responsible for triggering trait-mediated indirect effects [1,13]. With growing awareness of the role played by chemical information in shaping species interactions has come a realization that alteration of the background “odorscape” can potentially disrupt chemical communication by altering or masking the chemical cues, and this disruption may cascade through the community [14–16]. [SEP] Justify:

Output: The text contrasts the claim by explaining how many larval anurans (which are amphibians) respond to predators by making changes in behavior, morphology, and life history. This adaptive response demonstrates that amphibians do have methods of defending themselves from predators, thereby contradicting the claim that they possess no such methods.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Codon usage bias Different species use different codons with different frequencies, and there will be certain p0. 08 is defined as the optimal codon. Phylogenetic relationships of were aligned using MAFFT v 7. 308 [89] implemented in 2021. (ML) analysis and (BI) were employed for the phylogenomic reconstruction of Juglandaceae. The best-fit nucleotide substation model for ML and BI analysis was determined by Modeltest v3. 7 [90], in which the complete plastomes data was GTR + I + G and BI analyses were performed using the RAxML-HPC v8. 1. 11 and MrBayes v3. 2. 3 online tools available from the web server [91, 92]. The ML analysis was conducted with default settings with 1000 bootstrap replicates. BI trees were produced with the setting of 5,000,000 generations, under model with one cold and three incrementally heated (MCMC) run simultaneously [92] in two parallel runs sampling every 1000 generations. The first 25% of the trees were discarded as burn-in. The remaining trees were used for generating the consensus tree. Evolutionary analysis of Juglandaceae plastomes We observed Ks (synonymous), Ka (non-synonymous) substitution, and Ka/Ks ratio using pairwise alignment of protein-coding sequences of Morella rubra and other 50 selected species of Juglandaceae. We used M. rubra as the reference in each pair of alignments to make pairwise alignments with every gene. 2021 was used to extract 80 common protein-coding genes, and DnaSP v6. 0 was used to calculate the Ka and Ks substitutions. In addition, in order to detect the selection pressure on whole plastid genes with different functions, CDS genes were divided into photosynthesis-related, self-replication-related, and other functional genes (Table S1). Finally, we plotted boxplot graphs of the Ka/Ks values of CDS genes based on different functional classifications or taxonomic groups, and marked the significance of the differences between the groups. All analyses were conducted in R version 4. 3. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses codon usage bias, phylogenetic relationships, and evolutionary analysis of Juglandaceae, without any mention of artifacts or insights into past cultures.


Input: Task: corroborate the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: 666 p = 0. 001 NS DOI: 10. 7717/peerj. 3865/table-2 have identified bacteria with unusually large numbers of shared genes with archaea after accounting for the effect that genome size has on the number of shared genes (Fig. 5A). In general, these unusually large numbers of shared genes can be explained by horizontal gene transfer from archaea to bacteria (Figs. 4 and 7). More specifically, (hyper)thermophilic and anaerobic archaea are most likely to transfer genes to bacteria that live in high-temperature and anoxic habitats respectively (Fig. 7), though the genes transferred between anoxic and high temperature archaea and bacteria do differ (Table 2). In contrast, aerobic mesophiles appear to engage in very little inter-domain horizontal gene transfer. The most likely explanation for these results is that the (hyper)thermophilic and anaerobic organisms whose genomes were included in this study were isolated from environments (e. g. , hot springs, oil wells, sediments) with high population densities where cells are in close proximity and therefore more likely to exchange genes. This study suggests that bacteria inhabiting bodies of water are less likely to contain genes transferred from archaea and that rates of horizontal gene transfer would be greatly underestimated if based only on aquatic organisms. Furthermore, we have demonstrated the importance of adjusting for genome size when investigating other factors associated with the number of genes shared among genomes. Due to this genome size adjustment, this study is the first to be able to examine the effect of environment on horizontal gene transfer between archaea and bacteria on a broad scale. 1-5 of data used in analyses DOI: 10. 7717/peerj. 3865/supp-1 from the upper 95% CI for shared genes split into : 10. 7717/peerj. 3865/supp-2 Figures 1–7 DOI: 10. 7717/peerj. 3865/supp-3 We would like to thank Devine for statistical advice and Cedar McKay for computer support. authors declare there are no competing interests. Clara A. Fuchsman, Collins and William J. Brazelton conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper. conceived and designed the experiments, wrote the paper, reviewed drafts of the paper. A. [SEP] Justify:

Output: The text corroborates the claim by explaining that horizontal gene transfer from archaea to bacteria can account for unusually large numbers of shared genes. It specifically mentions that this transfer mechanism varies in likelihood depending on the environmental conditions and organisms involved, supporting the idea that horizontal gene transfer allows bacteria to acquire new traits.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: A number of studies show that a wide variety of anthropogenic pollutants commonly found in surface waters can impair chemoreception [17–18], even when present at low, sublethal concentrations. Dissolved metals, surfactants, pesticides, nanop1. Basic water quality parameters for the three water sources used in this study. assays were conducted in polyethylene washtubs (30 x 45 x 15 cm deep) filled with 7 L of water, drawn from the appropriate treatment. Five gray treefrog tadpoles were added to each washtub and allowed to acclimate 30 minutes before the initial behavioral assay was begun. We used tadpole activity level as our index of predator avoidance, as studies have shown that a reduction in activity is an adaptive response to dragonfly predators [25]. Activity was assayed both before treatment cues were added and after cue addition. Activity assays consisted of 20 second observations for each microcosm, with each microcosm observed in sequence. This observation cycle was repeated ten times for each observation bout, yielding 200 seconds of observation per microcosm for each bout. For each microcosm, the number of tadpoles active during the 20 second observation were counted, with any displacement movement scored as activity, and individual tadpoles were not scored more than once. The number of active tadpoles was divided by the total number of tadpoles (generally five) to yield the proportion of tadpoles that were active, and then the proportions were averaged across observations to yield an overall average activity level for a microcosm. Following the initial observation bout, predator cues were added, as described below, and post-cue observations began 30 minutes after cue addition. A total of 3 post-cue observation bouts were conducted, one 30 minutes after cue additions, one three hours after cue additions, and one 24 hours after cue additions. Preliminary analyses did not detect any effect of time after cue addition on activity, so we calculated an average activity per 20-second observation, based on all post-cue observations (which summed to ten minutes per microcosm), and used this value in all subsequent analyses. All observations were conducted by a single observer blind to treatment assignments. Predator cues were generated by individually housing larval dragonflies in 12 drinking cups holding 80 ml of water each. Dragonfly cups were filled with water drawn from the appropriate water type treatment. [SEP] Justify:

Output: The text contrasts the claim by describing an experiment involving gray treefrog tadpoles, which used activity level as an index of predator avoidance. Specifically, it notes that a reduction in activity is an adaptive response to dragonfly predators, indicating that amphibians do indeed have methods of defending themselves from predators.


Input: Task: pass the claim using the given text. Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: 0 ( Divergence-time estimation and fossil calibration We estimated the divergence time of Juglandaceae species based on 80 coding sequences (CDSs), combined with the calibration of four fossils (Table S9)[24, 70–73, 93–96]. The nucleotide substitution model is the same as the MrBayes parameters mentioned above. Before setting to model, set the molecular clock to log normal relaxation Molecular clock. For the MCMC program, the chain length was 5 × 108 generations, sampling every 10,000 generations. All options were set in BEAUTi v1. 10. 4, exported as an XML file, and run in BEAST v1. 10. 4 [97]. We checked the convergence of the Markov chains in Tracer v. 1. 6 ( and combined the chains after removing a burn-in of the first 50% generations. The effective sample sizes (ESS) exceeded 200 for all parameters. The program FigTree v1. 4. 3 ( was used to visualize mean node ages and highest posterior density (HPD) intervals at 95% (upper and lower) for each node and to estimate branch lengths and divergence times. Declarationsauthors thank Dr. Zhi-(CAS of of Sciences, Yunnan, China), for the help in the material collection. Authors' contributions YH: performed data analysis and drafted the manuscript; XJJ: conceived the study, designed the experiments, reviewed the paper; CYZ: collected the species of sample, performed the experiments; PL: collected and identified the species of sample; HHM: conceived the study, funding acquisition, collected and identified the species of sample, data curation. YHZ: conceived the study, funding acquisition, reviewed the manuscript critically. All authors have read and agreed with the contents of the manuscript. study was funded by the Foundation of China (42171063, 31800309) and the Technology and Project (LGN21C020007) Availability of data and materials Sequence data that support the findings of this study have been deposited in the under accession number CNP0005522. Ethics approval and consent to participate The collection of all samples completely complies with national and local legislation permission. Plant samples used in the study were not included in the list of national key protected plants and were not collected from the national park or nature reserve when we collected them. [SEP] Justify:

Output: The text is irrelevant to the claim as it discusses genetic divergence time estimation and the methodology for analyzing coding sequences from plant species, without any mention of artifacts, past cultures, or insights into daily lives.


Input: Task: pass the claim using the given text. Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: Fuchsman, Collins, and were all supported as IGERT trainees in Astrobiology under NSF grant 05-04219. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 2011. Horizontal gene exchange in environmental microbiota. Frontiers in Microbiology 2 2006. The marine viromes of four oceanic regions. PLOS Biology 4(11):e368 ämpfer P, Staley JT. 2006. Psychromonas ingrahamii sp. nov. a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice. of Systematic and 56:1001-1007. 2010. A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase. 12:2904-2917 Bates ST, Berg-. 2011. Examining the global distribution of dominant archaeal populations in soil. 5:908-917. 1991. Understanding bacterial biofilms. Trends in Biotechnology 9:138-143 Boto L. 2009. Horizontal gene transfer in evolution: facts and challenges. Proceedings of the B: 277:819-827 Brochier-Armanet C, Deschamps P, López-García P, Zivanovic Y, Rodríguez-Valera F, Moreira D. 2011. Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea. 5:1291-1302 Chang Y--öker -P, Lapidus A. 2011. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21) Standards in 5:97-111 Christensen H, Hansen M, Sørensen J. 1999. Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe. Applied and 65:1753-1761 Clarke KR. 1993. Non-parametric multivariate analyses of changes in community structure. of Ecology 18:117-143 Cordero OX, Hogeweg P. 2009. The impact of long-distance horizontal gene transfer on prokaryotic genome size. [SEP] Justify:

Output: The text is largely irrelevant to the claim as it mainly lists various studies and authors related to microbiology without directly addressing or supporting the idea of horizontal gene transfer as a mechanism for trait acquisition in bacteria. Although it mentions 'horizontal gene transfer' in a general context, it does not provide information or evidence that corroborates the claim.


Input: Task: contrast the claim using the given text. Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: Predators were placed in cups and fed one gray treefrog tadpole each 12 hours in advance of cue additions. Cues were transferred by removing the dragonfly from the cup and transferring the contents to the appropriate microcosm housing gray treefrog tadpoles. Each behavioral assay consisted of 24 independent replicates (washtubs) randomly assigned to the six treatment combinations of predation risk and water type. Assays were repeated, using fresh animals and water collections, on four dates, yielding a total of 96 independent observations for the overall experiment. We analyzed the effects of predator cues and water type on activity level with a factorial analysis of variance. A significant predator cue x water type interaction term would provide support for the experimental hypothesis. Because four independent assays were conducted, and there were biological reasons to believe that treatment effects may change across dates, we entered assay date into the model as an additional factor. In addition, we used the pre-cue activity level as a covariate in the model. The omnibus ANOVA was followed with three focused one-way ANOVA’s, performed separately for each water type, testing whether cell means differed for predator and no predator treatments. Activity data were log transformed prior to analysis to promote homoscedasticity and meet the assumptions of ANOVA. Raw data are provided in S1 Table. In presenting results, we calculate the percent reduction in activity as ((% activity without predators)–(% activity with predators)) (% activity without predators). ResultsDragonfly cues had a large effect on tadpole activity, as mean activity was reduced from 33% in the absence of predator cues to 21% in the presence of predator cues, a highly significant depression (Table 2). However, the effect of predator cues on tadpole activity depended on water treatment (Fig 1). Predator cues induced a 49% reduction in activity for tadpoles in tap water, a 29% reduction for tadpoles in river water, and a 24% reduction for tadpoles in wastewater effluent, yielding a significant interaction between the effects of predator cues and water type (Table 2). One-way ANOVA’s testing predator effects within each water type reveal that cues had highly significant effects on tadpoles housed in tap water (F1,30 = 17. 3, P < 0. 001), but predator cues had at best marginally significant effects on tadpoles housed in river water (F1,30 = 3. [SEP] Justify:

Output: The text contrasts the claim by providing evidence that gray treefrog tadpoles exhibit a significant behavioral response to predator cues, indicating that they have a method of defense through changes in their activity level when predation risk is perceived. Specifically, the results show that tadpoles significantly reduced their activity in the presence of predator cues, demonstrating their ability to respond defensively to threats.