Input: Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: Info-disruption: pollution and the transfer of chemical information between organisms. Evol. 2007; 22: 374–9. pmid:17433848 View 18. Olsen KH. Effects of pollutants on olfactory mediated behaviors in fish and crustaceans. In: Breithaupt T. and Thiel M. , editors. in Crustaceans, New York: Springer; 2011. 530. 19. Lürling M. Infodisruption: pollutants interfering with the natural chemical information conveyance in aquatic systems. In: Brönmark C, Hansson L-A, editors. in Aquatic Systems. Oxford: Press; 2012. 271. 20. Lawler SP. Behavioural responses to predators and predation risk in four species of larval anurans. Anim Behav. 1989; 38:1039–1047. View 21. . Costs and benefits of a predator-induced polyphenism in the gray treefrog Hyla chrysoscelis. Evolution. 1996; 50:583–593. View 22. . Threat of predation negates density effects in larval gray treefrogs. Oecologia. 2004; 138:532–538. pmid:14722747 View 23. . Predator-induced morphological changes in an amphibian: predation by dragonflies affects tadpole shape and color. Oecologia. 1997; 109:615–621. View 24. . Trait-mediated interactions: influence of prey size, density and experience. J Anim Ecol. 2008; 77: 478–486. pmid:18312336 View 25. Skelly DK. Activity level and the susceptibility of anuran larvae to predation. Anim Behav. 1994; 47:465–468. View 26. Blaxter JHS, Hallers-Tjabbes CCT. The effect of pollutants on sensory systems and behavior of aquatic animals. Aquat Ecol. 1992; 26:43–58. View 27. . Blinded by the stink: Nutrient enrichment impairs the perception of predation risk by freshwater snails. Ecol Appl. 2010; 20:2089–95. pmid:21265443 View 28. . Responses of wild fishes to alarm chemicals in pristine and metal-contaminated lakes. Zool. 2004; 82:694–700.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: The complete chloroplast genome sequence of Ampelopsis: gene organization, comparative analysis, and phylogenetic relationships to other Angiosperms. Sci. 2016;7:341. doi: 10. 3389/fpls. 2016. 00341. Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets. Syst Biol. 2007;56(3):412–430. doi: 10. 1080/10635150701408523. Molecular fingerprints resolve affinities of Rhynie chert organic fossils. Nat Commun. 2023;14(1):1387. doi: 10. 1038/s41467-023-37047-1. Fossil data support a pre-Cretaceous origin of flowering plants. Evol. 2021;5(4):449–457. doi: 10. 1038/s41559-020-01387-8. Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective. Genomes. 2007;3(4):363–378. doi: 10. 1007/s11295-006-0078-5. Palmer JD. Comparative organization of chloroplast genomes. Genet. 1985;19:325–354. doi: 10. 1146/annurev. ge. 19. 120185. 001545. Comparison and evolutionary analysis of chloroplast genomes in hemiparasitic plants of the Santalaceae. Breeding. 2022:1–30. Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus. BMC Genom Data. 2022;23(1):46. doi: 10. 1186/s12863-022-01064-8. Sueoka N. Near homogeneity of PR2-bias fingerprints in the human genome and their implications in phylogenetic analyses. J Mol Evol. 2001;53(4–5):469–476. doi: 10. 1007/s002390010237. Biogeographic history of Pterocarya (Juglandaceae) inferred from phylogenomic and fossil data. J Syst Evol. 2024. doi: 10. 1111/jse. 13055.

Output: pass


Input: Claim: Horizontal gene transfer is a mechanism by which bacteria can acquire new traits. [SEP] Text: The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proceedings of the of Sciences of the of America 102:18147-18152. 2002. Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes. Journal of 55:260-264 Nelson-. 2012. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proceedings of the of Sciences of the of America 109:20537-20542 Nelson--Chávez önheit. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517:77-80 Podell S, Gaasterland T. 2007. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. 8 2008. A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics 9:419. 2006. Viruses of the Archaea: a unifying view. Microbiology 4:837-848. 2016. Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters. Leeuwenhoek, of General and 109:855-868. 2011. Differences in lateral gene transfer in hypersaline versus thermal environments. BMC 11:199 Schippers A, Kock D, Höft C, Köweker G, Siegert M. 2012. Quantification of microbial communities in subsurface marine sediments of the black sea and off namibia. Frontiers in Microbiology 3 2011. Harvesting evolutionary signals in a forest of prokaryotic gene trees. and Evolution 28:1393-1405. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and 75:7537-7541. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241-244. 1999. Genome phylogeny based on gene content. 21:108-110. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41. 2005.

Output: corroborate


Input: Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: Despite above mentioned reports about the induction of fungal defense effector genes upon challenge with bacterial competitors and animal predators, it is not clear how specific these responses are, since almost no signals, receptors, and signaling pathways responsible for these responses are known. This is in contrast to plants and animals, in which sophisticated and multilayered systems of receptors and signaling pathways responsible for the recognition of antagonist-associated molecular patterns or effectors and the induction of antagonist-specific innate defense responses have been identified [31]. While mere wounding triggers the production of fungal defense effectors in some cases [5, 29], there are a few reports about antagonist-associated molecular patterns perceived by fungi. These patterns include cell wall fragments [32] and quorum-sensing signal molecules [33] in the case of bacteria and nematode developmental signal molecules in the case of animals [34]. Besides these soluble signal molecules or patterns, physical contact between the fungus and the antagonist appears to be required for induction of defense [23, 25]. With regard to pattern recognition receptors, plants and animals use two related sets of receptors, namely Toll-like receptors (TLRs) and nucleotide oligomerization domain (NOD)-like receptors (NLRs) for the extracellular and intracellular perception of signals, respectively [30, 35]. Binding of the molecular patterns by these receptors is often mediated by leucine-rich repeat (LRR) domains. Besides the well-characterized G-protein coupled receptors for endogenous sex pheromones, only a few reports of fungal receptors for specific biotic signals exist. Interestingly, the chemotropic sensing of host plant signals by the plant pathogenic fungus Fusarium oxysporum was recently demonstrated to be mediated by the sex pheromone receptor [36], suggesting that these receptors may have a broader specificity. None of the over 600 presently known fungal genome sequences, however, appear to encode TLRs. Hyphal growth of the animal-pathogenic yeast Candida albicans was shown to be triggered by direct interaction of bacterial muramyl dipeptides (MDPs) with the LRRs of an intracellular fungal receptor protein containing, in addition, a protein phosphatase and an adenylate cyclase domain [32].

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus. Sci. 2022;13:990064. doi: 10. 3389/fpls. 2022. 990064. Phylogenetic resolution in Juglans based on complete chloroplast genomes and nuclear DNA sequences. Sci. 2017;8:1148. doi: 10. 3389/fpls. 2017. 01148. Chloroplast genome dequence of Pigeonpea (Cajanus cajan (L. ) Millspaugh) and Cajanus scarabaeoides (L. ) thouars: genome organization and comparison with other Legumes. Sci. 2016;7:1847. doi: 10. 3389/fpls. 2016. 01847. . Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. . 1987;84:9054–8. doi: 10. 1073/pnas. 84. 24. 9054. . Complete chloroplast genomes of Chinese wild-growing Vitis species: molecular structures and comparative and adaptive radiation analysis. Protoplasma. 2020;258(3):559–571. doi: 10. 1007/s00709-020-01585-y. Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PLoS One. 2012;7(5):36869. doi: 10. 1371/journal. pone. 0036869. Complete chloroplast genome sequence of Clivia miniata and its characteristics. Sinica. 2020;47:2439–2450. doi: 10. 16420/j. issn. 0513-353x. 2020-0466. The complete chloroplast genome of Carya cathayensis and phylogenetic analysis. Genes (Basel). 2022;13(2):369. doi: 10. 3390/genes13020369. The chloroplast genome of Carya illinoinensis: genome structure, adaptive evolution, and phylogenetic analysis. Forests. 2020;11(2):207. doi: 10. 3390/f11020207. .

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in access Published: 12 April 2024 Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the ‘woody clade’ in Jia1 na1, Shuying Wang1 na1, Jinjin Hu1 na1, Ke Miao1,2, Yongjiang Huang1 & …Yunheng Ji1 Show authors BMC 104. 79 and 100. 23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4. 56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected. ConclusionsMolecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships. reports BackgroundThe core task of plant phylogenetics is to recover the tree of life for Plantae [1,2,3]. Although recent molecular phylogenetic studies have greatly improved our understanding of the angiosperm tree of life, some nodes remain notoriously recalcitrant [4,5,6,7,8]. Notably, the taxonomic affinities of such phylogenetically recalcitrant lineages have been markedly debated among previous morphology-based classification systems [e. g. , 9, 10–14]; and in recent molecular phylogenetic studies, the relationships between these nodes and related taxa were either poorly resolved or significantly incongruent [e. g. , 2, 7, 15–17]. Several lines of evidence suggest that these phylogenetically recalcitrant nodes may have undergone some evolutionarily complex events, such as radiative diversification, morphological convergence, and ancient hybridization, which most likely resulted in the absence of synapomorphies and/or phylogenetic conflicts inferred from different datasets [e. g.

Output: corroborate


Input: Claim: Amphibians have no method of defending themselves from predators. [SEP] Text: The original dogma that innate immune systems are not able to build up an immunological memory has recently been reconsidered both for plants and animals, and epigenetic histone modifications have been implicated in this process [47, 60]. To our knowledge, the only reports about persistence of an up-regulated defense response in mycelia in the absence of the antagonist, a phenomenon referred to in plants and animals as priming, are two studies by Rohlfs and coworkers [26, 58]. In these studies, the authors show that grazing by D. melanogaster larvae and the soil arthropod F. candida induces resistance of the mycelium toward grazing by these predators even after a period of 6 hours without grazing. These results suggest that the induction of the chemical defense in fungi is preserved for some time to protect the mycelium from further damage by predation. There is no data on the spatial distribution of this defense response in the mycelium, however. Interestingly, the induction is dependent on the master regulator of secondary metabolism, the LaeA-velvet system known to act via histone methylation [19], suggesting an epigenetic mechanism for defense gene induction and priming. Accordingly, induction of defense-related metabolic gene clusters in A. nidulans by bacteria was shown to involve histone acetylation [61]. What is the ecological significance of fungal defense? Only a few studies, amongst the two above-mentioned studies of A. nidulans [26, 58], have addressed the ecological significance of fungal defense in terms of fungal resistance toward grazing. Previous to these studies, it had been shown that A. nidulans mutants lacking the master regulator of secondary metabolism LaeA and transformants overexpressing the transcription factor RsmA are more susceptible to grazing by D. melanogaster larvae and more resistant to grazing by F. candida, respectively [44, 62]. Accordingly, aflatoxin production correlated with the fitness of different Aspergillus flavus isolates with regard to grazing by D. melanogaster larvae [29]. Relevance and impactFuture in-depth characterization of the fungal innate defense against microbial competitors and animal predators is not only important in terms of basic research, e. g. , the evolution of innate defense in eukaryotes, but also in terms of applied research.

Output: pass


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Completion of the chloroplast genomes of five and their contribution to chloroplast phylogeny. Sci. 2017;7:1955. doi: 10. 3389/fpls. 2016. 01955. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms. Evol. 2013;5(4):688–698. doi: 10. 1093/gbe/evt042. Kress WJ. Plant DNA barcodes: applications today and in the future. J Syst Evol. 2017;55(4):291–307. doi: 10. 1111/jse. 12254. Insights into comparative genomics, codon usage bias, and phylogenetic relationship of species from Biebersteiniaceae and Nitrariaceae based on complete chloroplast genomes. Plants (Basel). 2020;9(11):1605. doi: 10. 3390/plants9111605. . The complete chloroplast genomes of Echinacanthus species (Acanthaceae): phylogenetic relationships, adaptive evolution, and screening of molecular markers. Sci. 2019;9:1989. doi: 10. 3389/fpls. 2018. 01989. lyrata genome sequence and the basis of rapid genome size change. Nat Genet. 2011;43(5):476–481. doi: 10. 1038/ng. 807. . Codon usage pattern and genetic diversity in chloroplast genomes of Panicum species. Gene. 2021;802:145866. doi: 10. 1016/j. gene. 2021. 145866. Mutation bias is the driving force of codon usage in the Gallus gallus genome. DNA Res. 2011;18(6):499–512. doi: 10. 1093/dnares/dsr035. Variation and selection on codon usage bias across an entire subphylum. PLOS Genet. 2019;15(7):1008304. doi: 10. 1371/journal. pgen. 1008304. Identification and phylogenetic analysis of five Crataegus species (Rosaceae) based on complete chloroplast genomes.

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: , 4, 18–20]. The “woody clade” in Saxifragales (WCS), as defined by Jian et al. [21], comprises four woody families exclusively occurring in the Northern Hemisphere, i. e. , Altingiaceae (one genus, eight species) [22], Cercidiphyllaceae (one genus, two species) [23], Daphniphyllaceae (one genus, 30 species) [24, 25], and Hamamelidaceae (27 genera, 120 species) [7, 26]. The WCS represents one of the phylogenetically recalcitrant nodes in the angiosperm tree of life. The taxonomic affinities of these four families (as shown in Tables 1 and 2) are also contentious in the morphology-based classification systems proposed by Hutchinson [10], Cronquist [11], Dahlgren [12], Thorne [13], and Takhtajan [14]. This suggests a lack of robust morphological synapomorphies that unite them [21, 27]. Although previous studies have successfully recovered the phylogenetic backbone of Saxifragales and consistently resolved the WCS as a monophyletic group with strong support [8, 21, 27,28,29,30,31,32,33], the unresolved interfamilial relationships for Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae continue to be a subject of debate. Theoretically, the inconsistencies regarding the deep relationships of the WCS imply that it might have been subject to some evolutionarily complex events during its early evolution [16, 17, 19]. Table 1 Comparison of the order-level taxonomic placements of the four families within the “woody clade” in Saxifragales among previous morphology-based classification systemsFull size tableTable 2 Taxonomic studies of HamamelidaceaeFull size tableGiven that fossils represent the remains of past plants, they have the capacity to unveil intermediate evolutionary connections from the geological past, thereby offering valuable evidence for comprehending the evolution of the tree of life [34,35,36,37]. The combination of molecular and fossil evidence is recommended as an efficient approach for inferring the evolutionarily complex events that might result in phylogenetic recalcitrance in the angiosperm tree of life [16, 30, 38, 39].

Output: corroborate


Input: Claim: Reptiles are not capable of any form of parental care for their offspring. [SEP] Text: NHSA Dialog. 2009;3(1):75-80. Crossref31. Brigance HS. 1, 2022. Glascoe FP. infant and toddler screen: standardization and validation. J Pediatr. 2002;23(3):145-150. CrossrefPubMed33. JMP - John’s Macintosh Project. 5, 2022. Parental adverse childhood experiences and pediatric healthcare use by 2 years of age. J Pediatr. 2019;211:146-151. CrossrefPubMed35. Zero to Three. of of Infancy and Early Childhood: (DC:0–3R). ERIC Clearinghouse; 2005. 36. . Three questionnaires to detect psychosocial problems in toddlers: a comparison of the :SE, and. Acad Pediatr. 2013;13(6):587-592. CrossrefPubMed37. æver MS. Parent report measures of infant and toddler social-emotional development: a systematic review. Fam Pract. 2017;34(2):127-137. CrossrefPubMed38. -Isser A, et al. Factors associated with whether pediatricians inquire about parents’ adverse childhood experiences. Acad Pediatr. 2016;16(7):668-675. CrossrefPubMed39. Marie-Mitchell A, Kostolansky R. A systematic review of trials to improve child outcomes associated with Experiences. Prev Med. 2019;56(5):756-764. CrossrefPubMed40. . Effectiveness of a home intervention for perceived child behavioral problems and parenting stress in children with in utero drug exposure. Adolesc Med. 2001;155(9):1029-1037. CrossrefPubMed41. -Gowan MJ. A randomized controlled trial of : a comprehensive home-based intervention translating research into Practice. Child Dev. 2011;82(1):193-208. CrossrefPubMed42. . Identifying adverse childhood experiences in pediatrics to prevent chronic health conditions. Pediatr Res. 2020;87(2):362-370. CrossrefPubMed43. Review of tools for measuring exposure to adversity in children and adolescents. J Care. 2018;32(6):564-583. CrossrefPubMed2022. This 4.

Output: pass


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Planta. 2021;254(1):14. doi: 10. 1007/s00425-021-03667-4. Mutation pressure and natural selection on codon usage in chloroplast genes of two species in Pisum L. (Fabaceae: Faboideae). . 2019;30(4):664–673. doi: 10. 1080/24701394. 2019. 1616701. Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species. PeerJ. 2021;9:12173. doi: 10. 7717/peerj. 12173. Analysis on codon usage bias of the chloroplast genome of Camellia osmanth. Journal of University of Forestry & Technology. 2022;42:178–186. Kawabe A, Miyashita NT. Patterns of codon usage bias in three dicot and four monocot plant species. Sys. 2003;78:343–352. doi: 10. 1266/ggs. 78. 343. An extensive analysis on the global codon usage pattern of baculoviruses. Arch Virol. 2008;153(12):2273–2282. doi: 10. 1007/s00705-008-0260-1. Roychoudhury S, Mukherjee D. A detailed comparative analysis on the overall codon usage pattern in herpesviruses. Virus Res. 2010;148(1–2):31–43. doi: 10. 1016/j. virusres. 2009. 11. 018. Analysis of codon usage patterns in Taenia pisiformis through annotated transcriptome data. Res Commun. 2013;430(4):1344–1348. doi: 10. 1016/j. bbrc. 2012. 12. 078. Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species. PeerJ. 2020;8:e8251. doi: 10. 7717/peerj. 8251. Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L. J Biol. 2007;49:246–254. doi: 10. 1111/j. 1744-7909. 2007. 00404.

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: Recently, genome-scale sequence data, particularly plastid genomes (plastomes), have been increasingly used to solve historical puzzles in plant phylogenetics [e. g, 8, 28, 29, 40–48]. In general, phylogeny inferred from uniparentally inherited plastomes reflects only the maternal (or, in some cases, paternal) relationships, as compared to the more comprehensive evolutionary history recovered through the phylogenetic analyses of biparentally inherited nuclear genomes [49]. Nevertheless, the comparison of tree topologies inferred from plastomes and nuclear genomes can facilitate the determination of phylogenetic discordance between plastid and nuclear datasets (cytonuclear discordance), providing robust evidence to infer whether the evolution of the taxa in question has involved evolutionarily complex events, such as incomplete lineage sorting and hybridization [50, 51]. Recent phylogenomic studies have yielded valuable insights into the deep relationships within the WCS. Based on nuclear genome data generated by target-capture sequencing and RNA-seq, Folk et al. [28] recovered the phylogenetic backbone of the WCS with high-resolution and well-supported interfamilial relationships. In contrast, previous plastome-based phylogenetic analyses of the WCS taxa have demonstrated tree topologies with low support [52, 53] and inconsistent inter-familial relationships [32, 33]. Consequently, the family-level maternal relationships within the WCS remain ambiguous, providing weak evidence for detecting cytonuclear discordance in the deep relationships within the WCS. Notably, the maternal inheritance of plastomes in the WCS as well as in the Saxifragales has been verified by the investigations of several species including Hamamelis virginiana, Heuchera micrantha, and Tolmiea menziesii [54, 55]. By expanding the taxonomic sampling of the WCS to include the majority of genera, the objectives of this study are to recover a robust maternal backbone phylogeny of the WCS through analysis of plastome sequence data. Based on a time-calibrated phylogenetic framework, fossil evidence, and a comparison of plastome (this study) and nuclear [28] phylogenies, evolutionarily complex events putatively responsible for the phylogenetic recalcitrance of the deep phylogeny of the WCS were inferred.

Output: corroborate


Input: Claim: All spiders spin webs, regardless of their species. [SEP] Text: (D) Quantification of L2 mis-expression experiments in adult flies. L2 neurons were considered ‘isolated’ if they were the only clone within a column, and surrounded by columns without other MARCM clones. Thirteen of the sixteen L2 neurons mis-expressing dFezf-HA mis-targeted to M3. Of the thirteen mis-targeting neurons seven were ‘isolated’. These findings strongly support that dFezf cell autonomously instructs L2 mis-targeting in mis-expression experiments. Figure 5 with 3 supplements Download asset Open asset DFezf regulates a complex program of cell surface gene expression. (A and B) MARCM was performed to generate and specifically label single wild type or dFezf1 L3 neurons at 40 hr APF. L3 clones were labeled with a nuclear reporter (H2A-GFP) and a transmembrane reporter (myr::tdTomato) by 9–9 GAL4. (A) A representative confocal image shows that L3 neurons are the only cell type labeled by both GFP (green) and tdTOM (magenta). Photoreceptor neurons (R1-R8) (blue, mAB24B10) are labeled as a reference for the lamina and medulla. Scale bar = 20 microns. (B) A representative FACS plot shows that L3 neurons expressing H2A-GFP and myr::tdTomato separated as a tight cluster from background cells (100K events are shown). (C) A heat map (row scaled) of differentially expressed genes that includes data from all samples. Each row represents the normalized expression of a differentially expressed gene, and each column represents a sample. Presenting the data in this manner shows that samples clearly separate based on genotype, and that large fractions of differentially expressed genes are either up or downregulated. (D) Table showing dpr genes that are differentially expressed between wild type and dFezf null L3 neurons. The genes are listed in order of significance (padj). The top three most significant DE genes overall, dprs 17, 13, and 1 are shown in red, and the rest of the genes are shown in green. TPM (transcripts per million mapped reads) values are averages across all samples for a given genotype.

Output: pass


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: x. Factors affecting synonymous codon usage bias in chloroplast genome of Ramsey. Online. 2011;7:271–278. doi: 10. 4137/EBO. S8092. Chloroplast genome analysis of resurrection tertiary relict Haberlea rhodopensis highlights genes important for desiccation stress response. Sci. 2017;8:204. doi: 10. 3389/fpls. 2017. 00204. Complete chloroplast genome of Tetragonia tetragonioides: molecular phylogenetic relationships and evolution in Caryophyllales. PLoS One. 2018;13(6): 0199626. doi: 10. 1371/journal. pone. 0199626. Keller J, Rousseau-Gueutin M, Martin GE, et al. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. DNA Res. 2017;24(4):343–358. doi: 10. 1093/dnares/dsx006. Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus. Ecol Evol. 2021;11(19):13401–13414. doi: 10. 1002/ece3. 8063. Comparative and phylogenetic analysis of the complete chloroplast genomes of three Moutan species (Paeoniaceae). Front Genet. 2020;11:980. doi: 10. 3389/fgene. 2020. 00980. Large-scale phylogenetic analyses reveal fagalean diversification promoted by the interplay of diaspores and environments in the Paleogene. Syst. 2014;16(3):101–110. doi: 10. 1016/J. PPEES. 2014. 03. 001. . Fruits of Juglandaceae from the Eocene of South America. Syst Bot. 2016;41:316–328. doi: 10. 1600/036364416X691830. Comparative flower development of Juglans regia, Cyclocarya paliurus and Engelhardia spicata: homology of floral envelopes in Juglandaceae. Linn Soc. 2016;181(2):279–293. doi: 10.

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: 1Phylogenetic relationships within the “woody clade” in Saxifragales. The tree was built using maximum likelihood (ML) and Bayesian inference (BI) methods, based on 78 plastid protein-coding genes from 64 different species. (A) Cladogram. (B) Phylogram based on ML. (C) Phylogram based on BI. Numbers superimposed on the branches indicate bootstrap support (%) and posterior probability. FO, Fothergilleae; HA, Hamamelideae; EU, Eustigmateae; CO, Corylopsideae; LO, LoropetaleaeFull size imageFig. 2Phylogenetic relationship within the “woody clade” in Saxifragales. The tree was constructed using maximum parsimony (MP) methods, based on 78 plastid protein-coding genes of 64 species. Numbers superimposed on the branches indicate bootstrap support (%). FO, Fothergilleae; HA, Hamamelideae; EU, Eustigmateae; CO, Corylopsideae; LO, LoropetaleaeFull size imageEstimation of divergence timeFossil-calibrated molecular dating (Fig. 3) showed that the diversification of the WCS crown groups initiated at ∼104. 79 Ma, corresponding to the divergence of Altingiaceae. Subsequently, the divergence of Hamamelidaceae and the stem lineage ancestor of Cercidiphyllaceae and Daphniphyllaceae occurred at ∼103. 22 Ma, followed by the separation of Cercidiphyllaceae and Daphniphyllaceae at ∼100. 23 Ma. Despite the ancient origins of Altingiaceae, Daphniphyllaceae, and Cercidiphyllaceae during the early Cretaceous, their crown ages were dated at ∼37. 8 Ma (Altingiaceae), ∼29. 19 Ma (Daphniphyllaceae), and ∼4. 16 Ma (Cercidiphyllaceae), respectively. Within Hamamelidaceae, the estimated ages for the origins of the subfamilies Exbucklandiodeae and Mytilarioideae were approximately 100. 3 Ma and 96. 98 Ma, respectively; in contrast, their crown ages were dated at around 55. 03 Ma and 39.

Output: corroborate


Input: Claim: All spiders spin webs, regardless of their species. [SEP] Text: (A–D’) In the lamina, lamina neurons are born in a wave (Anterior = oldest, Posterior = youngest). The yellow dashed lines in (A–C) indicate the anterior-posterior region of the lamina where NetB expression is first observed. and D’ anterior-posterior is indicated by A-P. (A) At 24 hr APF, NetB (green) was expressed in the anterior side of the developing lamina (to the left of the yellow dashed line) containing the oldest lamina neurons. NetB was expressed in L3 neurons (magenta, dFezf-FLAG). The youngest L3 neurons on the posterior side of the lamina that had not turned on NetB expression are indicated by asterisks. (B) At 24 hr APF, NetB (green) was detected in L4 and L5 neurons (magenta, α-bsh) in the oldest region of the lamina (to the left of the yellow dashed line). NetB (green) was not detected in L1 neurons (blue, α-svp, asterisks in the anterior region). (C) Consistent with findings shown in B, at 24 hr APF NetB (green) was expressed in the oldest L4 neurons (magenta) in the anterior region of the lamina (left of the dashed yellow line). L4 neurons were labeled using an L4-specific driver (31C06-LexA, LexAop-myr::tdTomato). At this stage 31C06-LexA drives expression in a small population of L4 neurons in the anterior region of the lamina. R1-R6 axons (blue. mAB24B10) provided a reference for the lamina. The image shown here is taken from a pupa that is slightly older than in A and B, as NetB is expressed in nearly all the lamina neurons in the field of view. (D and D’) NetB (green) was not expressed in L2 neurons (magenta) at 24 hr APF. L2 neurons were visualized using a specific driver (16H03-LexA, LexAop-myr::tdTomato) that drives expression in the most anterior (oldest) L2 neurons at this stage.

Output: pass


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: 1111/boj. 12413. Manning WE. The classification within the Juglandaceae. Bot Gard. 1978;65:1058–1087. doi: 10. 2307/2398782. Phylogeny, taxonomy, and biogeography of Pterocarya (Juglandaceae). Plants (Basel). 2020;9(11):1524. doi: 10. 3390/plants9111524. Complete chloroplast genome of the threatened Rhoiptelea chiliantha (Juglandaceae s. l. ). Resour. 2018;11(3):317–319. doi: 10. 1007/s12686-018-1021-4. Manchester SR. The fossil history of the Juglandaceae. Bot Gard. 1987;21:1–137. Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Syst Biol. 2012;61(2):289–313. doi: 10. 1093/sysbio/syr116. Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes. Nat Commun. 2023;14(1):617. doi: 10. 1038/s41467-023-36247-z. Heřmanová Z, Kvaček J, Friis EM. Budvaricarpus serialis Knobloch &Mai, an unusual new member of the normapolles complex from the of the Czech Republic. Plant Sci. 2011;172(2):285–293. doi: 10. 1086/657278. Wolfe JA. Some aspects of plant geography of the northern hemisphere during the and Tertiary. Bot Gard. 1975;62:264–279. doi: 10. 2307/2395198. Tiffney BH. Perspectives on the origin of the floristic similarity between America. J Arnold Arbor. 1985;66:73–94. doi: 10. 5962/BHL. PART. 13179. Tiffney BH. land bridge: its importance in Tertiary and modern phytogeography of the northern hemisphere. J Arnold Arbor. 1985;66:243–273. doi: 10.

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: 58 Ma. Additionally, the divergence between subfamilies Disanthoideae and Hamamelidoideae was estimated to have occurred approximately 93. 93 (Ma), and the divergence of the five tribes within subfamily Hamamelidoideae was dated at around 86. 6 Ma for tribe Eustigmateae, approximately 83. 41 Ma between tribes Corylopsideae and Loropetaleae, and about 83. 07 Ma between tribes Fothergilleae and Hamamelideae; by comparison, the crown ages of the tribes Fothergilleae, Eustigmateae, Corylopsideae, and Loropetalea were estimated to be around 42. 38 Ma, 40. 44 Ma, 39. 84 Ma, and 33. 16 Ma, respectively. Fig. 3Fossil-calibrated molecular phylogenetic dating of the “woody clade” in Saxifragales. The chronological estimates were performed using MCMCtree with the maximum likelihood (ML) tree as a topological constraint. Numbers superimposed on the branches represent mean divergent ages and 95% confidence interval of each node, respectively. The red dots represent the secondary calibration and fossil-calibration nodes. The divergence time and timeline are indicated in million years ago (Ma). FO, Fothergilleae; HA, Hamamelideae; EU, Eustigmateae; CO, Corylopsideae; LO, LoropetaleaeFull size imageDiscussionThe fossil-calibrated plastome phylogeny (Fig. 3) showed that all three of the WCS monotypic families (i. e. , Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae) are deep clades, considering the ancient origin of their stem lineage ancestors (104. 79–100. 23 Ma) versus the relatively hysteretic divergence of their crown groups (37. 81–4. 61 Ma). Within Hamamelidaceae, a similar pattern of early stem ages (100. 3-83. 07 Ma) compared to relatively later crown ages (55. 03–33.

Output: corroborate


Input: Claim: Spiders are incapable of hunting and rely solely on their webs to catch prey. [SEP] Text: s Cite this review as (2020) #1 of "Orb-weaving spiders are fewer but larger and catch more prey in lit bridge panels from a natural artificial light experiment (v0. 2)". PeerJ Reviewer 2 · Feb 21, 2020 Basic reporting I am happy with how the manuscript has been restructured Experimental design The experimental design is now easier to follow, and I am satisfied with the author's responses to my queries Validity of the findings The data have been better placed in the appropriate context, and the conclusions are now better supported by the rest of the manuscript Cite this review as (2020) #2 of "Orb-weaving spiders are fewer but larger and catch more prey in lit bridge panels from a natural artificial light experiment (v0. 2)". PeerJ 0. 2 (PDF) Download author's response letter - submitted Feb 6, 2020 Version 0. 1 (original submission) · Dec 24, 2019 · We have received the reviews from two reviewers, and both of them have suggested major revisions. Please make the revisions and resubmit. · Dec 18, 2019 Basic reporting The 138. [this one is particularly relevant given the implications for food restriction] Kleinteich, A. , & Schneider, J. M. (2011) Developmental strategies in an invasive spider: constraints and plasticity. Ecological Entomology, 36, 82-93. And also, the Heiling studies already cited in the paper. At present it’s hard to link the results to what this means for the species or ecology. Greater engagement in this regard would be helpful. Third, particularly given the first point above, I urge greater caution and constraint in how the results are presented and interpreted. For example, the title and abstract are much too broad given the study (more detail on this below). Additional comments: Title – needs to be better constrained and described… at present it reads like a review which this is not, best to have a title that captures the essential result and in the proper context, e. g.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: 5962/BHL. PART. 13183. . The use of geological and paleontological evidence in evaluating plant phylogeographic hypotheses in the Tertiary. Plant Sci. 2001;162(S6):3–17. doi: 10. 1086/323880. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science. 2001;292(5517):686–693. doi: 10. 1126/science. 1059412. . Cenozoic continental climatic evolution of Central Europe. . 2005;102:14964–14969. doi: 10. 1073/pnas. 050526710. Jin JH. fossil fruits from the of Hainan Island, China. Palynol. 2009;153(1–2):150–152. doi: 10. 1016/j. revpalbo. 2008. 07. 010. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020;21(1):241. doi: 10. 1186/s13059-020-02154-5. CPGView: A package for visualizing detailed chloroplast genome structures. Resour. 2023;23(3):694–704. doi: 10. 1111/1755-0998. 13729. VISTA: computational tools for comparative genomics. Res. 2004;32(issue):273–279. doi: 10. 1093/nar/gkh458. Vega-Trejo R, de Sex-specific inbreeding depression: A meta-analysis. Ecol Lett. 2022;25(4):1009-1026. doi: 10. 1111/ele. 13961. REPuter: the manifold applications of repeat analysis on a genomic scale. Res. 2001;29:4633–4642. doi: 10. 1093/nar/29. 22. 4633. Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Evol. 2017;34(12):3299–3302. doi: 10. 1093/molbev/msx248. Hershberg R, Petrov DA.

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: 16 Ma) was observed in the subfamilies Exbucklandioideae, Mytilarioideae, and Disanthoideae, as well as in the five tribes (Corylopsideae, Eustigmateae, Fothergilleae, Hamamelideae, and Loropetaleae) belonging to the subfamily Hamamelidoideae. As suggested in previous studies [8, 16, 21, 27, 29], the presence of deep stems within these clades may be attributed to a lack of cladogenesis or extensive extinction of closely related taxa during their early evolutionary processes. Fossil evidence has disproven the hypothesis that cladogenesis was absent during the early evolution of the aforementioned WCS clades. The most typical example is Altingiaceae, within which three extinct genera, i. e. , Paleoaltingia, Protoaltingia, and Microaltingia, have been documented from the late Cretaceous of [56,57,58]. Similarly, three extinct genera (Allonia, Androdecidua, and Archamamelis) have been discovered in Hamamelidaceae [59,60,61]. Among them, Allonia and Androdecidua were delineated based on floral remains from the late Cretaceous of the and were assigned to tribe Loropetaleae of subfamily Hamamelidoideae [60, 62]. Archamamelis was also established based on floral remains with in situ pollen from the late Cretaceous of Sweden and was assigned to tribe Hamamelideae of subfamily Hamamelidoideae [59, 62]. Within Cercidiphyllaceae, four extinct genera (Jenkinsella, Joffrea, Nyssidium, and Trochodendroides) have been reported [63,64,65,66]. Among them, a Joffrea species has been documented from the late Paleocene of Canada [64]; 10 Jenkinsella, 13 Nyssidium, and 60 Trochodendroides species [67, 68] have been discovered across the spanning from early Cretaceous to Eocene epochs [67, 68]. Most of these extinct taxa have been identified through well-preserved reproductive organs utilizing various approaches such as scanning electron microscopy and cladistic analysis to explore their taxonomic affinities.

Output: corroborate


Input: Claim: Spiders are incapable of hunting and rely solely on their webs to catch prey. [SEP] Text: “Orb-weaver spiders are fewer and smaller in unlit bridge panels from a natural artificial light experiment” (or something like this) Abstract – at present, about half of the abstract is speculative… I would reduce this in favor of focusing more on the methods and results (there is essentially nothing in the abstract about the methods) line 10 – the relationship between insects and light is complex, e. g. Owens, A. C. , & Lewis, S. M. (2018). The impact of artificial light at night on nocturnal insects: A review and synthesis. Ecology and Evolution, 8, 11337-11358. I think this paragraph and the following two could be better developed line 36 – is a week of data enough? line 40 – what’s the light brightness? Is it fluorescent? More details needed here regarding the light source line 42 – “unlit” line 55 – so were all the species recorded (not just collected) Larinioides sclopetarius? And if so, why not make this clear in the abstract? If not, what else was observed? Line 75 – what was the prey? And is number of prey most appropriate here instead of say, prey mass? lines 106-108 – what’s the range of spiders in lit and unlit? line 114 – I would interpret this as there not being effect (it isn’t a problem of the statistics) line 120 – what family? line 152 – I presume that the idea here is that lit webs are attracting more prey. This is discussed in the intro but should be made explicit here as well. But also, there are more webs in unlit conditions, thus it could just be that there are more webs competing for the same number of insect prey and webs in lit conditions take advantage of this (rather than there simply being more prey) line 169 – I don’t think it’s very clear, particularly given that you didn’t measure prey. The main point of this sentence is fine but I would suggest being cautious about claims like this. Figs 3-5: Increase font size of axes to improve readability Cite this review as (2020) #1 of "Orb-weaving spiders are fewer but larger and catch more prey in lit bridge panels from a natural artificial light experiment (v0. 1)".

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Selection on codon bias. Genet. 2008;42:287–299. doi: 10. 1146/annurev. genet. 42. 110807. 091442. . Solving the riddle of codon usage p5044. doi: 10. 1093/nar/gkh834. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Evol. 2013;30(4):772–780. doi: 10. 1093/molbev/mst010. Posada D. ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Res. 2006;34:700–3. doi: 10. 1093/nar/gkl042. . A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008;57(5):758–771. doi: 10. 1080/10635150802429642. Ronquist F, Huelsenbeck JP. els. Bioinformatics. 2003;19(12):1572–1574. doi: 10. 1093/bioinformatics/btg180. The antiquity of Cyclocarya paliurus(Juglandaceae) provides new insights into the evolution of relict plants in subtropical China since the late Early Miocene. J Biogeogr. 2016;43(2):351–360. doi: 10. 1111/jbi. 12635. Larson-Johnson K. Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales. New Phytol. 2016;209(1):418–435. doi: 10. 1111/nph. 13570. Pterocaryoid fruits (Juglandaceae) in the Paleogene of and their evolutionary and biogeographic significance. Bot. 1982;69(2). doi: 10. 2307/2443015. . Corylus, Carpinus, and Palaeocarpinus (Betulaceae) from the of northwestern North America. Plant Sci. 2003;5:807–822. doi: 10. 1086/376816. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees.

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: The aforementioned evidence strongly supports that cladogenesis did occur during the early evolution of WCS clades. Although no Daphniphyllaceae fossil has yet been found, the currently available fossil evidence robustly supports the conclusion that the deep stems of the afore-mentioned WCS clades can be attributed to the prominent extinction of their closely related taxa during their initial evolutionary stages. Notably, the majority of extinct genera within the WCS (i. e. , Allonia, Androdecidua, Archamamelis, Paleoaltingia, Protoaltingia, and Microaltingia) disappeared from the fossil record after the Cretaceous period [56, 57, 59, 60, 62, 69]. Although the survival of Jenkinsella, Nyssidium, and Trochodendroides (Cercidiphyllaceae) extended to the Eocene, their species diversity had significantly declined since the Cretaceous/Paleocene boundary [65] and completely vanished prior to the Oligocene era [63,64,65, 67]. The fossil evidence suggests the extinction events in the early evolution of the WCS might have primarily occurred around the Cretaceous/Paleocene boundary. This temporal coincidence aligns with Earth’s most recent mass extinction event when over 75% of species became extinct [70,71,72]. For phylogenetic analysis, the families Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae exhibit extremely deep stems that may expose them to long-branch attraction [73], potentially leading to erroneous grouping in evolutionary trees. Previous studies have demonstrated that MP phylogenies are more susceptible to long-branch attraction compared to BI and ML phylogenies [74, 75]. Consistent with this, our MP phylogeny revealed distinct tree topologies concerning the interfamilial relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae when compared to ML and BI phylogenies (Figs. 1 and 2). These findings suggest that the reconstruction of the WCS’s phylogeny could be influenced by long-branch attraction effects, resulting in a certain degree of bias in topological estimation [73, 75, 76]. Consequently, significant extinction events during the early evolution of the WCS might contribute significantly to the recalcitrance observed in resolving deep relationships within this clade.

Output: corroborate


Input: Claim: Spiders are incapable of hunting and rely solely on their webs to catch prey. [SEP] Text: PeerJ Reviewer 2 · Dec 23, 2019 Basic reporting This is a well-written manuscript that clearly explains the experiment using appropriate language. The figures are relevant and easy to understand. The literature relating to spiders foraging under artificial light at night is well referenced. However, the introduction requires a lot more context for the effects of light pollution broadly, particularly for its physiological effects which have potential consequences for body condition and mortality, both of which are directly relevant to this experiment. More information is also needed for the basic biology of web building, and the importance of different lighting technologies to provide context to these results. Experimental design This is a well-designed and simple experiment that neatly tests a hypothesis, and these connections are clearly communicated. The introduction provides context for why investigating web building, abundance and body condition of an orb-weaver in the field is important. Some of the methods require more description, such as the choice of web for architecture measurements, and better justification is required for the use of body condition residuals. It would also be useful to explain why this paper is important given that a similar experiment was performed by Heiling & Herberstein (1999). Validity of the findings The discussion provides a useful interpretation of the results, supported by the literature. This would be improved by expanding on explanations of results, given improved context in the introduction (e. g. physiological damage from ALAN), and providing better comparisons with cited literature (e. g. differences with Zygiella, similar result found for tetragnathids, effects of light type, etc. ). Additional comments This is a very interesting study, and you have done a good job communicating your results and linking your results to your hypotheses. My main suggestions for improvement are to provide a more comprehensive introduction and a more cohesive discussion. Annotated reviews are not available for download in order to protect the identity of reviewers who chose to remain anonymous. Cite this review as (2020) #2 of "Orb-weaving spiders are fewer but larger and catch more prey in lit bridge panels from a natural artificial light experiment (v0. 1)". PeerJ Submission (PDF) - submitted Dec 9, 2019 All text and materials provided via this peer-review history page are made available under a Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: BMC Evol Biol. 2007;7:214. doi: 10. 1186/1471-2148-7-214. Additional DeclarationsNo competing interests reported. Supplementary FilesFigureS1. tifFig. S1. Alignment visualization of the 13 Engelhardia plastomes. Using E. anminiana as a reference. The vertical scale indicates the percentage of identity, ranging from 50 to 100%. Arrows indicate the annotated genes and their transcriptional direction. The different colored boxes correspond to exons, tRNA or rRNA, and noncoding sequences (CNSs). FigureS2. tifFig. S2. Alignment of 13 Engelhardiaplastomes. The E. anminiana genome is shown at the top as the reference genome. The overall sequence similarities were shown above and the collinear DNA components were indicated by the green, red, and white blocks below. FigureS3. pdfFig. S3. Insertion and deletion events detected in plastomes of different Juglandaceae species based on the ML tree. FigureS4. pdfFig. S4. The RSCU of 80 protein-coding genes of 50 Juglandaceae plastomes. The red color indicate higher RSCU values, and the blue color indicate lower RSCU values. The horizontal axis represents amino acids and their coding codons, while the vertical axis represents different species. FigureS5. pdfFig. S5. Gene correlation coefficients among Juglandaceae plastomes. The red color indicate higher RSCU values, and the blue color indicate lower RSCU values. Meanwhile, the larger the circle, the greater the absolute value. The left half was displayed as a heat map, and the right half was the corresponding numerical value. FigureS6. pdfFig. S6. The phylogenetic tree of Juglandaceae species based on plastomes. Tree were constructed by maximum likelihood (ML) and Bayesian inference (BI) with bootstrap values or posterior probabilities above the branches, respectively. The blue one is the species of Juglandoideae, the green one is the species of Engelhardioideae subfamily, and the red one is the species of Rhoipteleoideae subfamily. TableS1. docxTableS2. docxTableS3. docxTableS4.

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: In addition, Altingiaceae, Cercidiphyllaceae, and Hamamelidaceae have stipules and winged seeds, distinguishing them from the non-stipulate leaves and wingless seeds of Daphniphyllaceae [23, 24, 26, 84], supporting the transitional position of Cercidiphyllaceae as a phylogenetic link between Daphniphyllaceae and the clade Altingiaceae + Hamamelidaceae. The high levels of consistency between the nuclear genome phylogeny and morphological traits suggest that the cytonuclear discordance observed in the WCS phylogeny might have been caused by ancient interfamilial hybridization. Interestingly, a previous study [56] showed that interfamilial hybridization might have occurred during the early evolution of the WCS. Based on scanning electron microscopic investigations, tricolpate-reticulate pollen was found to attach to the stigmas of the fossil pistillate inflorescences of Microaltingia, an extinct Altingiaceae genus from the late Cretaceous of the [56, 85]. Within the WCS, tricolpate-reticulate pollen exists in Hamamelidaceae, Cercidiphyllaceae, and Daphniphyllaceae but not in Altingiaceae [56, 85]. The fossil evidence implies that ancient hybridization between Altingiaceae and closely related families might be feasible. Therefore, chloroplast capture [17, 82] caused by ancient hybridization is likely a reasonable interpretation of the phylogenetic discordances detected in the deep relationships within the WCS. Concordant with fossil evidence [56, 57, 59, 60, 62, 69, 86], which suggests that the early evolution of the WCS might have experienced radiative lineage diversification, the results of divergence time estimation indicated that the WCS underwent rapid divergence in the crown groups during the early Cretaceous, leading to the occurrence of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (within ∼4. 56 Ma, and between 104. 79 and 100. 23 Ma).

Output: corroborate


Input: Claim: All bats feed on blood like vampire bats. [SEP] Text: edited by Theodore H. Fleming, Liliana M. Dávalos and Marco A. R. of Chicago Press, 2020Cloth: 978-0-226-69612-6 | Electronic: 978-0-226-69626-3DOI: 10. 7208/chicago/9780226696263. 001. 0001 of (cloth, ebook) DeGruyter Multi-eBooks (formerly NetLibrary) (UPSO) more than two hundred species distributed from California through Texas and across most of mainland Mexico, Central and South America, and islands in the Caribbean Sea, the Phyllostomidae bat family (American leaf-nosed bats) is one of the world’s most diverse mammalian families. From an insectivorous ancestor, species living today, over about 30 million years, have evolved a hyper-diverse range of diets, from blood or small vertebrates, to consuming nectar, pollen, and fruit. Phyllostomid plant-visiting species are responsible for pollinating more than five hundred species of neotropical shrubs, trees, vines, and epiphytes—many of which are economically and ecologically important—and they also disperse the seeds of at least another five hundred plant species. Fruit-eating and seed-dispersing members of this family thus play a crucial role in the regeneration of neotropical forests, and the fruit eaters are among the most abundant mammals in these habitats. Coauthored by leading experts in the field and synthesizing the latest advances in molecular biology and ecological methods, is the first overview in more than forty years of the evolution of the many morphological, behavioral, physiological, and ecological adaptations in this family. Featuring abundant illustrations as well as details on the current conservation status of phyllostomid species, it is both a comprehensive reference for these ecologically vital creatures and a fascinating exploration of the evolutionary process of adaptive radiation. . Fleming is professor emeritus of biology at the University of Miami, where he worked for thirty years. Among his recent books are of Life, both published by the University of Chicago Press, and Is an Island. Liliana M. Dávalos is professor of conservation biology at University. She is coeditor of of Cocaine and coauthor of the 2016 Report. Marco A. R.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Corresponding Author: Institute for Genetics of (IfGH), Münster (Germany) E-Mail guiscard. seebohm@ukmuenster. de -2 in Infertility? Frank Tüttelmannb. Schreibera,d Bernhard Wünschd Nathalie Strutz-Seebohma a, Institute for Genetics of (IfGH), Münster, Münster, Germany, bInstitute of Reproductive Genetics, University of Münster, Münster, Germany, cIstituto di Biofisica, delle Ricerche, Genova, Italy, dInstitute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany, eCentre of and Andrology, Department of Clinical and Surgical Andrology, Münster, Münster, • • Sperm • Male infertility Abstract Background/Aims: Neanderthals, although well adapted to local environments, were rapidly replaced by anatomically modern humans (AMH) for unknown reasons. Genetic information on Neanderthals is limited restricting applicability of standard population genetics. Methods: Here, we apply a novel combination of restricted genetic analyses on preselected physiological key players (ion channels), electrophysiological analyses of gene variants of unclear significance expressed in Xenopus laevis oocytes using two electrode voltage clamp and transfer of results to AMH genetics. Using genetic screening in infertile men identified a loss of CLC-2 associated with sperm deficiency. Results: Increased genetic variation caused functionally impaired Neanderthals CLC-2 channels. Conclusion: Increased genetic variation could reflect an adaptation to different local salt supplies at the cost of reduced sperm density. Interestingly and consistent with this hypothesis, lack of CLC-2 protein in a patient associates with high blood K+ concentration and azoospermia. IntroductionDNA comparisons between Neanderthals and AMH have indicated that Neanderthals mated with and share more genetic variants with non-Africans than with Africans [1]. At around 41,000 years ago, modern humans bearing the so-called Protoaurignacian culture spread into southern Europe leading to the demise of Neanderthals [2].

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: The mutually supporting evidence suggests that, in addition to ancient hybridization, incomplete lineage sorting (the stochastic sorting of ancestral sequence polymorphisms) [16, 51] resulted from the process of radiative diversification during the early evolution of WSC may contribute to the observed phylogenetic recalcitrance in the deep relationships of the WCS. ConclusionThe WCS is a representative of the phylogenetically recalcitrant node in the angiosperm tree of life, within which the deep relationships remain poorly resolved. Based on a broad taxonomic sampling at the genus level across the four currently recognized families in the WCS, we recovered a robust maternal backbone phylogeny for this group. Based on molecular and fossil evidence, this study indicates that the early evolution of the WCS might have undergone radiative diversification of crown groups in the early Cretaceous, ancient hybridization, and prominent extinction events during the transition between the Cretaceous and Paleocene. These events most likely resulted in the phylogenetic reconstruction of the deep relationships within the WCS being adversely affected by incomplete lineage sorting, cytonuclear discordance, and long-branch abstraction, which inevitably led to serious topological estimation biases. Nevertheless, possible ancient hybridization and incomplete lineage sorting in the early evolution of the WCS inferred in this study are merely based on the phylogenetic incongruence between plastid and nuclear genomic data, and other supporting evidence is still lacking. This inference needs to be validated through in-depth analysis of the conflicts between the species tree and gene trees using nuclear genome data containing multiple single-copy orthologous genes. MethodsTaxonomic sampling, DNA extraction, and Illumina sequencingAccording to the most recent taxonomic revision of Altingiaceae [22], Cercidiphyllaceae [23], Daphniphyllaceae [24, 25], and Hamamelidaceae [26], the WCS comprises approximately 173 species belonging to 30 genera [7, 22, 23, 25]. In this study, 56 species representing all three genera in the three monotypic families (Cercidiphyllaceae, Daphniphyllaceae, and Altingiaceae) and 15 out of the 27 currently recognized genera in Hamamelidaceae were sampled.

Output: corroborate


Input: Claim: All bats feed on blood like vampire bats. [SEP] Text: Mello is professor of ecology at the University of São Paulo, Brazil. He served as the president of the and is the author, in Portuguese, of Sobrevivendo na Ciência: Manual para a Jornada do Cientista. “Phyllostomid Bats: A Radiation (edited by Theodore H. Fleming, Liliana M. Dávalos, and Marco A. R. Mello) is an outstanding book. The diversity of detailed information is exceptional. The book’s twenty-four 1. Overview of - Theodore H. Fleming, Liliana M. Dávalos, Marco A. R. MelloDOI: 10. 7208/chicago/9780226696263. 003. 0001[adaptive radiation;biological diversity;Phyllostomidae]This book discusses in detail the adaptive radiation of American leaf-nosed bats (Phyllostomidae), the most diverse family morphologically, behaviorally, and trophically of all bats. It is divided into five major sections that cover the family’s evolution, classification, and historical biogeography; many aspects of its basic biology; its trophic, population, and community ecology; and its conservation. Because of its biological diversity, this family can serve as a model system for understanding the adaptive radiation of mammals in the last half of the Cenozoic Era. (pages 3 - 6)This 2. Setting the Stage: Climate, Geology, and Biota - Theodore H. FlemingDOI: 10. 7208/chicago/9780226696263. 003. 0002[climatic changes;coevolution;frugivory;gleaning insectivory;geological changes;nectarivory;sanguinivory]I review changes in the climate, geology, and biota of the tropics and subtropics over the past 30 million years to understand the physical and biological opportunities and constraints phyllostomid bats faced during their adaptive radiation. This radiation occurred during a period of decreasing atmospheric CO2 levels, decreasing global air and sea temperatures, and increasing climatic seasonality that have led to the evolution of a great diversity of vegetation types, including tropical dry forests, montane forests, savannas, and deserts.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: However, the reasons why Neanderthals were replaced by AMH are heavily discussed and include factors such as environmental changes leading to reduced genetic variation [3], changes in language [4], infectious diseases [5], behavior-cultural reasons [6], and anatomical and physiological cues [7, 8]. An additional driver for the Neanderthal demise may have been that they were simply outnumbered. Neanderthal populations were generally small in size and rather isolated, but shortly after the arrival of AMH, the human population increased tenfold for unknown reasons but AMH’s numerical supremacy may have driven Neanderthal replacement [9, 10]. Recently, the debate about what drove the extinction of Neanderthals has started to include physiological factors, such as metabolic peculiarities in Neanderthals’ lipid and glucose metabolism [7, 8]. Because such physiological issues are central players in current-day human health, they may have been even more critical for determining the survival of hominids like the small-group dwelling Neanderthals. Therefore, key elements of health in modern humans may have been relevant for Neanderthal fitness. We analyzed the rate of genetic variance in ion channel-encoding genes. Ion channels are such key players in human health and fitness, and certain human diseases called channelopathies arise from a series of ion channel genetic variants. Furthermore, and unsurprisingly, the majority of all current drugs on the market act directly or indirectly via ion channels. Therefore, ion channel gene variants represent perfect candidates for evolutionary drivers of fitness (or lack thereof). Materials and MethodsMutagenesis and Electrophysiology. Human CLCN2 was subcloned into pSGEM. hKv1. 5-eGFP was obtained by and mutagenesis was performed as described before [11]. All constructs were verified by Sanger sequencing. Xenopus laevis oocytes were obtained by Ecocyte (Dortmund, Germany). Linearized cDNA was transcribed using the mMessage mMachine kit (Ambion) and the constructs were expressed in oocytes by injection of 5 to 50 ng human CLC-2 cRNA according to the expression level of the channel. Oocytes were kept in a Barth solution containing (in mM) 90 NaCl, 10 HEPES, 2 KCl, 1 MgCl2, 1 CaCl2, pH 7. 5, for 3 days at 18°C.

Output: pass


Input: Claim: Fossil records provide critical evidence for understanding evolutionary processes. [SEP] Text: 2 Ma. In addition, the earliest fossils of the extinct genera Trochodendroides [66], Allonia/Androdecidua [60, 62], and Archamamelis [59, 61, 62] were chosen to constrain the stem ages of Cercidiphyllaceae (100. 5 Ma), Loropetaleae (83. 6 Ma), and Hamamelideae (83. 6 Ma), respectively. These fossils are either infructescences/fruits or well-preserved flowers with pollen [60, 61, 66], and their systematic positions have been robustly verified and extensively used for calibrating the phylogeny of angiosperms [e. g. , 29, 62, 105]. We used the ML tree as a topological constraint. The uncorrelated log-normal relaxed clock model was employed, with a Yule tree prior and under a GTR sequence substitution model as recommended by Paup v4. 0 [106]. The MCMC was run for 500 million generations, sampling a tree every 1000 generations, with the first 20% of trees being discarded as burn-in. The convergence of the MCMC stimulations was inspected using Tracer v1. 7. 1 [99]. The ESS of the estimated parameters was, in most cases, > 200, and it was always > 125. Files containing the sampled trees were combined and annotated using LogCombiner v1. 10. 4 and Treeannotator v1. 10. 4, respectively, using the BEAST package. The maximum clade credibility tree with median ages and 95% highest posterior density intervals for all nodes was visualized using Figtree v1. 3. 1 ( Data availability The complete plastomes generated in this study are available at the database, with the accession numbers being presented in Table S1.

Output: corroborate


Input: Claim: All bats feed on blood like vampire bats. [SEP] Text: Reinforcing the effects of temperature changes was the uplift of the major mountains in western North America, Central America, and western South America. Most of the extant diversity of noctilionoids is found on the Neotropical mainland in lowland forested habitats, which have existed in one form or another throughout the Americas since the late Cretaceous. A minority of species has evolved in more recent dry or arid habitats, in the mountains, or in the West Indies. Early phyllostomids were gleaning insectivores whose diets differed from those of other families of insectivorous bats. (pages 7 - 22)This 3. Phylogeny, Fossils, and Biogeography: History of (Chiroptera: Yangochiroptera) - Norberto P. Giannini, Paúl M. VelazcoDOI: 10. 7208/chicago/9780226696263. 003. 0003[phylogeny;fossils;Gondwana;behavioral ecology;echolocation]The superfamily Noctilionoidea comprises more than 230 species in 68 genera and is one of the most ecologically diverse groups of mammals, as its species consume almost the entire dietary spectrum known for terrestrial mammals, including insectivorous, omnivorous, carnivorous, piscivorous, nectarivorous, hematopagous, and frugivorous species. Here we 1) revisit the relationships of the superfamily with other groups of bats, and the family-level phylogenetic relationships within the group; 2) review the historical biogeography of the superfamily on the basis of phylogenies and the fossil record of the constituent noctilionoid families; and 3) provide an overview of the ecology of members of noctilionoid families, which collectively compose the most inclusive outgroup to the Phyllostomidae. Finally, we interpret the historical and ecological grounds and evolutionary context from which the Phyllostomidae diversified. (pages 25 - 42)This 4. Diversity and Discovery: A - Andrea L. Cirranello, Nancy B. SimmonsDOI: 10. 7208/chicago/9780226696263. 003. 0004[Phyllostomidae;species description;classification;taxonomic discovery]Taxonomy is central to modern biology.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Two electrode voltage-clamp was performed with a Turbotec10 amplifier (npi, Tamm, npi electronic, Germany) and freeware acquisition program GePulse (freely available at The recordings were performed at room temperature (20°C). To analyse the currents of wild type CLC-2 and and mutant CLC-2, oocytes were first pulsed to 60 mV to estimate the instantaneous activated current under resting conditions, and then they were activated with a long pulse to –140 mV. The following tail pulse to 60 mV induced a very reproducible current deactivation, which can be best described by standard double exponential kinetics. of the tail pulse indirectly reflects the functional expression level, and the ratio Iss/Imax reflects the preference of the channel for the open configuration [37]. Human embryonic kidney (HEK) 293 cells were transfected with 1 µg human Kv1. 5-eGFP cDNA (note: Kv1. 5 is encoded by gene KCNA5) and recorded in extracellular solution containing (in mM): 140 NaCl, 2 MgSO4, 2 CaCl2 and 10 HEPES/NaOH pH 7. 3 using the standard patch clamp technique. Intracellular solution was (in mM) 130 KCl, 2 MgSO4, 2 EGTA and 10 HEPES/NaOH pH 7. 3. Voltage protocol and data analyses are as follows: Wild type and mutant hKv1. 5 were elicited by 60 mV square pulses at a Vhold of -80 mV and current amplitudes were analyzed. Neanderthal variant calling. sequence contigs from six Neanderthal individuals (‘Feld1’, ‘Mez1’, ‘Sid1253’, ‘Vi33. 16’, ‘Vi33. 25’, ‘Vi33. 26’) mapped against human hg18 reference genome was downloaded from Tracks at UCSC (ftp://hgdownload. cse. ucsc. edu/gbdb/hg18/neandertal/seqAlis/all-hg18. bam). SNP and short indel calling was performed using the UnifiedGenotyper algorithm implemented in GATK software suite [12-14].

Output: pass


Input: Claim: Adaptive radiation explains the diversification of species in new environments. [SEP] Text: We then investigated whether the distribution of body size in Liolaemus has evolved around a given number of SVL optima (i. e. , whether stabilizing selection has promoted macroevolutionary convergences of the trait against one or more such peaks), using the ‘surface’ package in R [63, 64]. This surface method fits an adaptive radiation model in which lineages on a phylogeny may experience convergent shifts towards adaptive optima on a macroevolutionary Simpsonian landscape, importantly, without assumptions of whether some lineages correspond to particular optima [63, 64]. Based on an OU model [60] in which all species are pulled against a single adaptive optimum in morphospace, employs a stepwise model selection approach based on AICc, which allows for identification of the best model and the numbers and positions of adaptive peaks (i. e. , trait ‘regimes’), and hence, for convergence towards these optima over evolutionary time [63, 64]. We then modelled body size disparity through time (DTT). Based on size data from extant species (see above), this approach calculates the mean disparity for the trait over time, and compares the observed body size disparity with that expected under a null model of Brownian-motion by simulating body size evolution 10,000 times across the tree [12]. Then, the average body size disparity obtained from the real and the simulated data are plotted against node age to calculate the morphological disparity index (MDI). This index quantifies the overall difference in relative disparity for the trait among and within subclades (i. e. , differences in the range of variation) compared with the expectation under the null Brownian motion model [13, 62, 65]. Negative MDI values indicate lower than expected trait relative disparity under Brownian motion (i. e. , low average subclade relative disparity), which in turn indicates that most disparity occurs among subclades, and therefore, that they occupy smaller and more isolated areas of the morphospace [12]. In contrast, positive MDI values indicate that relative disparity among subclades shows stronger overlap in morphospace occupation [12]. Trait disparity analyses were conducted using the R package ‘geiger’ [62].

Output: corroborate


Input: Claim: All bats feed on blood like vampire bats. [SEP] Text: Although many researchers assume that most mammal taxa are already known—and have been for decades—this is not necessarily true for small mammals including bats. Examination of patterns of taxonomic discovery over the last 200+ years reveals that we are currently in a taxonomic “Golden Age” for phyllostomid bats with more than 40 species discovered and described since 2001. Although the pace of discovery was slow throughout the 1700s, by 1850 representatives from 10 of the 11 subfamilies that we recognize today had been described, 22 genera had been named, and 39 phyllostomid species had been identified as specimen collections were amassed in European institutions. However, it was not until the early 1900s that a peak in descriptions occurred, with more than 20 species still considered valid described in the decade between 1901-1910. Most taxa described in the 19th and 20th centuries were described by scientists based in Europe, but research activity and descriptions of new taxa shifted to institutions between 1950 and 2000. Since 2001, the majority of published species descriptions have been authored or co-authored by researchers from Central and institutions. (pages 43 - 62)This 5. Fragments and Gaps: Record - Nancy B. Simmons, Gregg F. Gunnell, Nicolas J. CzaplewskiDOI: 10. 7208/chicago/9780226696263. 003. 0005[diversification;extinction;fossils;Miocene;Paleogene;Phyllostomidae;Pleistocene;Pliocene;Holocene]While modern molecular phylogenetic studies can provide a framework for understanding relationships of phyllostomids to one another and their close relatives, it is only the fossil record that can provide calibration points for reconstructing the temporal pattern of diversification. Additionally, the fossil record can facilitate synthetic understanding of patterns of morphological change over time. The fossil record of Phyllostomidae definitely extends to the early Miocene (~ 21-19 Ma) of Panama, and may extend as far back as the late middle Eocene (~41 Ma) of Peru, but it is surprisingly incomplete before the Pleistocene. Crown group members of the extant subfamilies Phyllostominae and Lonchophyllinae are known from Miocene localities in the Neotropics.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: [15] was used to annotate the called variants with RefSeq gene names and to predict their impact and effect. Mutation rate per gene has been calculated as variant count per length of human gene coding sequence (total SNVs) as well as functional variant count per length of human gene coding sequence (non-syn SNVs). Any non-synonymous coding variants or insertions/deletions have been considered for further analyses. Resulting mutation rates of ion channel genes have been log10-transformed to fit a normal distribution as tested by Shapiro-Wilk normality test implemented in R (p-value = 0. 363). Mutation rates differing more than 2 standard deviations from mean of all analyzed ion channel genes have been considered as enriched mutation rates. ResultsBy analyzing the published Neanderthal genomes and comparing them with 33 human disease-linked ion channel genes, we identified a high rate of genetic variation of uncertain significance (GVUC) in Neanderthal Cl- channel encoding genes CLCN2 and, to a lower degree, in CLCN1 (Fig. 1A, B). 1 mutations associate with myotonia congenita, a rare disease characterized by muscle stiffness upon sudden forced movements [16, 17]. Regarding CLCN2, patients and knock-out mice with mutations in this gene show a more complex phenotype: CLC-2 dysfunction has been associated with retinal degeneration, leukodystrophy, and severe testicular degeneration [18-20]. Conversely, CLC-2 gain-of-function mutations have been shown to result in hyperaldosteronism type II; the increased aldosterone levels cause early-onset high blood pressure, predisposing affected individuals to potassium loss and potentially lethal cardiac arrhythmias [21, 22]. Fig. 1. Analysis of Neanderthal genetic variants of unclear significance (GVUC). All currently known Neanderthal GVUCs are analyzed in a selection of ion channels and Cl- transporters known to be associated with human disease. A. CLCN2 shows an increased number of GVUCs. Values for CLCN2 are magenta colored. B. The numbers of variants in Neanderthals and AMH were analyzed with respect to specific exchanged bases, and they show similar overall patterns. C. are positioned in highly conserved regions and therefore suggest functional relevance.

Output: pass


Input: Claim: Adaptive radiation explains the diversification of species in new environments. [SEP] Text: Red arrows indicate the position of the three body size peaks (in mm) identified by the surface analysis (see text for details)Full size image Our model-based analyses of body size diversification identified OU as the best approximation to the observed pattern of evolution of this trait in Liolaemus (Table 2). Therefore, our results suggest that body size diversification has been subject to stabilizing selection that has forced the expression of the trait around certain adaptive optima over time. and BM models were, respectively, the next best-fitted models, while the EB model was identified as the weakest approximation to describe the pattern of body size evolution (Table 2). Our subsequent convergence analyses of multiple body size peaks on a Simpsonian landscape revealed that three optima (or body size regimes) exist within Liolaemus, suggesting that species are pulled by stabilizing selection around the size optima 57. 96 mm, 80. 45 mm, and 87. 66 mm (Additional file 2: Figures S1 and S2). Table 2 Rates and modes of evolutionary diversification in Liolaemus body size based on comparisons of the fit of four evolutionary models. Fitted models are Brownian-motion (BM), Ornstein-Uhlenbeck (OU), Early-Burst (EB) and Delta. Best-fit of models based on (delta) bias-corrected Criteria (AICc)Full size table Finally, our analysis of trait-dependent macroevolutionary diversification identified a negative linear function as the best model. That is, diversification rates increase as a linear function of decreasing body size (Table 3). Table 3 QuaSSE trait-dependent lineage diversification in Liolaemus. Analyses based on selection from multiple models described by a linear, sigmoidal or hump-shaped function with (drift) and without a ‘drift’ or directional term added to the model fitting (see text for details). Best-fit of models based on (delta) bias-corrected Criteria (AICc)Full size table DiscussionRapid early bursts of phylogenetic, phenotypic and ecological diversification within a lineage entering a novel adaptive zone are central components of the definition of a process of adaptive radiation [2, 71].

Output: corroborate


Input: Claim: All bats feed on blood like vampire bats. [SEP] Text: phyllostomids exhibit dental morphology and body sizes suggesting that they were insectivores, but some may have been at least partially carnivorous or omnivorous, indicating that ecological diversification in the family was well underway in the Miocene. Large numbers of phyllostomid fossils are known from Pleistocene and Holocene deposits in Central America, South America, and the Caribbean, but no or Pliocene fossil phyllostomids are known, hence there is a ~10 million year gap in the fossil record. (pages 63 - 86)This 6. Phylogenetics and - Liliana M. Dávalos, Paúl M. : 10. 7208/chicago/9780226696263. 003. 0006[Andes;;dispersal;diversification;Interchange;Lonchorhina;Micronycterinae;Neotropics]Traditionally, the phylogeny of phyllostomids contained a few subfamilies sharing similar cranial and ecological traits. Family-wide genetic sequence data starting in the early 2000s, however, showed that this phylogeny obscured the taxonomy, biogeography, and evolution of ecological traits in the family. Current phylogenies strongly support the monophyly of 11 subfamilies, as well as most relationships among them. Nonetheless, the positions of several key groups are not well-supported and require further analyses, including: 1) Micronycterinae relative to Desmodontinae, 2) Lonchorhininae, and 3) the genus-level resolution of Miocene fossils. Historical biogeographic analyses have revealed a origin for most subfamilies; have inferred widespread and multi-continental distributions for ancient ancestors; and have rejected a special influence of Quaternary glaciations on recent speciation. These analyses have also confirmed North and Central America, as well as South America, as independent centers of diversification for some subfamilies (e. g. , Macrotinae), as well as within subfamilies (e. g. , Glossophaginae). These parallel centers of diversity might result from the absence of continuous dry habitat corridors between the continents, but this hypothesis has not been tested using phyloclimatic methods. (pages 87 - 104)This 7.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Typically, these GVUCs are filtered out in the process of genomic filtering leaving the genetic CLC-2 variations highly hypothetical. To exclude DNA degeneration as basis of Neanderthals genetic CLCN2 variation (Fig. 1A) we evaluated the pattern of base exchanges of Neanderthal gene variants. Neanderthal CLCN2 variants show a similar base pair exchange pattern compared to AMH, suggesting that we identified real variants rather than artifacts (Fig. 1B). Further, the CLCN2 sequence does not differ substantially in chemico-structural parameters (GC and AT content, intron/exon structure and length), meaning that the Neanderthal gene variants may have been present in living Neanderthals and potentially have impacted their lives (see below). are positioned in highly conserved regions of CLCN2, as shown by sequence alignments (Fig. 1C). CLCNx genes encode CLC-x proteins, a eukaryotic family of four Cl- anion channels (CLC-1, -2, -Ka, and -Kb) and five anion-H+ exchangers (CLC-3 to -7) containing 17 transmembrane α-helices [23]. CLCs are homo-dimers with separate active anion transport pathways in each subunit [24-27]. The structurally very similar prokaryotic and eukaryotic CLC anion-H+ exchangers have been crystallized [24, 28, 29], and we used these as templates to generate a structural model of CLC-2. With this model, we localized the position of several of the variants to highly sensitive regions of the CLC-2 channel protein: the transmembrane domain, which includes the selectivity filter and intracellular CBS domain (Fig. 2B). These findings suggest that the gene variants could result in impaired Cl- ion channel function. Fig. 2. Analyses of Neanderthal CLC-2 GVUCs. A. Examples of wild type (wt) and -2 currents (control = non-injected). Note: Mutant A506T is still inhibited by iodide, indicating that the current measured is still conducted by CLC-2 pores (data not shown). B. Neanderthal genetic variants were generated and expressed in Xenopus laevis oocytes.

Output: pass


Input: Claim: Adaptive radiation explains the diversification of species in new environments. [SEP] Text: g. , 23], which would explain their differences in radiation patterns. Ecological opportunity is, however, unlikely to be a feature of islands only. Instead, we argue that ecological opportunity is temporally episodic and dependent on the environmental (i. e. , ecological, geographic, climatic) stability of a landmass. Islands are in general more unstable [76], while continents (given their larger area) are more stable over time. Therefore, the emergence of ecological opportunity is more likely to be a function of landmass area, and hence, it may only be less frequent in continents. In fact, continents are known to have been scenarios for active adaptive radiations driven by emergence of ecological opportunity, for example, following mass extinctions [1–3, 72]. In line with these views, the prolific continental radiation of Liolaemus lizards has been suggested to be importantly explained by large-scale ecological opportunity [6, 35]. Adaptive radiations can be triggered by extrinsic factors such as the arise of new ecological opportunity via emergence of novel environments, and/or by intrinsic factors (‘key adaptive innovations’) that increase the availability of niches to a diversifying lineage [1–3, 7, 9]. Pincheira-Donoso et al. [6] suggested that the onset of this lizard radiation resulted from a combination of both scenarios. Extrinsically, the emergence and uplift of the Andes over the last ~25My [77, 78] created unprecedented novel ecological opportunity (an enormous new high-elevation ecosystem), which is known to have also promoted biodiversity proliferations in a variety of other organisms [79–82]. Intrinsically, given that low-temperature environments impose strong selection against reptile developing eggs in nests [83, 84], successful colonization of cold Andean climates demanded the evolution of prolonged embryo retention, i. e. , viviparity [6]. In support of this view, the overwhelming majority of cold-climate Liolaemus species are viviparous [6, 36, 85], and the multiple independent events of phylogenetic oviparity-to-viviparity transitions are strongly correlated with multiple independent invasions of colder environments during the lineage history [6].

Output: corroborate


Input: Claim: All bats feed on blood like vampire bats. [SEP] Text: Adapt or Live: Adaptation, Convergent Evolution, and Plesiomorphy - Liliana M. Dávalos, Andrea L. Cirranello, Elizabeth R. Dumont, Stephen J. : 10. 7208/chicago/9780226696263. 003. 0007[adaptation;dietary specialization;diversification;ecological theory of adaptive radiation;Ornstein-Uhlenbeck models;trophic level]A diversity of cranial phenotypes and feeding ecologies characterizes phyllostomid bats. However, many subfamilies share a similar insect-feeding morphotype, apparently stable over millions of generations. Is the diversity of phyllostomid traits adaptive, and does it contribute to species diversity in the family? We evaluate predictions from Simpson’s ecological theory of adaptive radiation, applied to comparative trait analyses since 2000. The shift to higher rates of taxonomic diversification at the base of Stenodermatinae, new skull architecture capable of great bite force despite small size, and a distinctive olfactory receptor profile make this subfamily a radiation by itself. The stenodermatine skull architecture also enables making leaf tents, a new roost adaptive zone that contributes to the diversity of this subfamily. The evolution of distinct trophic adaptive zones characterized by optima in cranial musculature and mechanical advantage shows that stenodermatines are not the only phyllostomid lineage responding to ecological opportunities. Instead, nectarivores have unique cranial traits and occupy their own trophic adaptive zone, while a subset of insectivores together with sanguivores share a similarly high trophic level. There's evidence of convergent and adaptive evolution in cranial traits associated with similar trophic levels, and adaptations coupled with dietary specialization in digestive and renal function. (pages 105 - 122)This 8. of in - Norberto P. Giannini, Lucila I. Amador, R. ArévaloDOI: 10. 7208/chicago/9780226696263. 003. 0008[body size;continuous character optimization;phylogenetic constraints;dietary shifts;phyletic trends;past character displacement]Body mass is the single most important factor affecting the biology of animals.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Analyses of currents of all Neanderthal CLC-2 gene variant channels compared to wt channel currents (± SEM) are shown. Several genetic variants resulted in functional alteration of CLC-2 channels. C. Structural modeling suggest that particularly the Neanderthal GVUCs in the trans-membrane region alter channel function. In order to address the functional effects of the respective gene variants directly, we generated individual Neanderthal CLCN2 gene variants and analyzed them functionally in Xenopus laevis oocytes (Fig. 2A, B). We found diverse functional effects as a result of the various gene variants. CLC-2 activates upon hyperpolarization and may contribute a Cl- efflux pathway to regulate the basolateral Cl- efflux in epithelial cells [30-32]. We found that the steady state CLC-2 currents were reduced by eleven variants and were increased by four variants. Further, CLC-2 channel gating is characterized by two processes that open the channel at negative voltages, reflecting opening of individual protopores (fast gate), and a slower mechanism that operates on both pores of the double-barreled channel [33-36]. Conversely, at positive voltages, the channel reaches its minimum open probability, and this probability can be affected by mutation [36] or by association with the glial-specific cell adhesion molecule GlialCAM [37, 38]. We found that four variant channels showed changes in gating kinetics and altered the minimum open probability (Fig. 3). Thus, overall 59. 3 % of the potential Neanderthal variants resulted in functional aberrations (41 % with loss-of-function and 15 % with gain-of-function, and 15% showed gating abnormalities, Fig. 3). To determine if the percentage of CLCN2 GVUCs that we identified as having functional consequences (59. 3%) coincides with this percentage for other Neanderthal ion channel genes, we examined potential Neanderthal variants of the alternative ion channel Kv1. 5 (Fig. 4): 63. 6 % (7 out of 11) of Kv1. 5 Neanderthal variants showed significant functional changes, suggesting that the number of Neanderthal gene variants correlates with the number of functionally relevant gene variants (Fig. 4).

Output: pass


Input: Claim: Adaptive radiation explains the diversification of species in new environments. [SEP] Text: Invasions of cold-climate Patagonia have followed exactly the same patterns, thus reinforcing the ‘key innovation’ nature of viviparity [6]. Remarkably, over 55 % of the Liolaemus species for which parity mode is known are viviparous [6, 85]. Therefore, this relatively young continental lineage is likely to have adaptively radiated driven by ecological opportunity, and about half of its exceptional diversity potentially evolved as a result of the viviparity innovation that allowed access to exploit such opportunities [6]. Interestingly, as indicated by Schulte et al. [36], our results also suggest that the enormous climatic crises caused by the Pleistocene do not seem to have had an important role in the diversification of Liolaemus lineages (Fig. 2). Our lineage through-time analyses support a density-dependent model of adaptive radiation, as shown by the DDL + E model identified as the best approximation for the diversification within Liolaemus. This analysis suggests that Liolaemus diversification has tended to decline over time as a function of accumulating species, although both the exponential and the decline phases of the diversification curve are only slightly pronounced (in fact, the Yule model was identified as the next best alternative; Fig. 2). These findings contrast with the model-based analysis of body size diversification, which identified the ‘early burst’ (EB) model as the less preferred alternative (and the OU as the best one), while the relative disparity through-time analysis returned a positive MDI value (i. e. , extensive trait diversification, but strong subclade overlap in the morphospace, [12]). Traditionally, negative MDI values are interpreted as consistent with phenotypic diversification during adaptive radiation [12, 13, 16, 86]. Therefore, in our analyses, the rates and trajectories of diversification are not consistent between lineage and phenotypic evolution (although a negative relationship between the two seems to have dominated the radiation history of this clade; Table 3). However, we argue that the high phenotypic diversification and morphospace overlap found in Liolaemus can in fact be consistent with a process of adaptive radiation. In this lineage, geographic overlap among main subclades tends to be limited [31, 36, 87], compared to other reptile radiations.

Output: corroborate


Input: Claim: All bats feed on blood like vampire bats. [SEP] Text: Small size is generally highly favorable for flying vertebrates; in addition to this constraint, echolocating bats are also restricted by the physics of call parameters. However, we find in a single group, the Noctilionoidea, virtually the entire size range found across all echolocating bats. Here we examine the evolutionary significance of this variation. We explore how the reconstructed body mass of the ancestral phyllostomid was inherited from noctilionoid ancestors, how size changed along the branches of the phyllostomid tree, and how size co-varied with characteristic evolutionary shifts in the ecology of phyllostomid bats. We found little change along the backbone of the phylogenetic tree and across major dietary transitions, many scattered increases and decreases of variable magnitude, and most variation concentrated in phyletic change in a few groups, especially vertebrate-specialized and frugivorous phyllostomids. These trends imply sustained selection acting over millions of years in a consistent direction, principally towards an increase in size. Initial stasis may have facilitated ecological transitions, while capacity for size change may have fueled intense directional selection within highly specialized lineages. Finally, diverging trends appear to reflect past character displacement. (pages 123 - 148)This 9. Structure and Function of Bat Wings: A View from the Phyllostomidae - Sharon M. Swartz, Justine J. AllenDOI: 10. 7208/chicago/9780226696263. 003. 0009[aerodynamics;biomechanics;elastin;flight;musculoskeletal;sensory;skin;wings;wing;morphology]Understanding the evolution of bat flight behavior and explaining the diversity in the structure of their wings requires examination of the functional organization and mechanical properties of wing tissues. In-depth structural analyses that consider multiple levels of organization can complement phylogenetically based comparative analyses, even if they do not sample a large number of taxa. In this 10. between Physiology and Diet - Ariovaldo P. Cruz-Neto, L. M. DOI: 10. 7208/chicago/9780226696263. 003.

Output: contrast


Input: Claim: Artifacts can provide insights into the daily lives of past cultures. [SEP] Text: Human loss-of-function mutations in CLCN2 have been associated with leukodystrophy [18] and azoospermia [19], suggesting that CLC-2 dysfunction can cause male infertility [39]. Consistently, CLC-2 knock-out mice also exhibited testicular degeneration, whereby their primary spermatocytes and later the spermatogonia degenerated, and the tubules contained abnormal Sertoli cells [39]. In order to verify the suggested critical role for CLC-2 function in normal spermatogenesis, we screened whole-exome sequencing data of 887 infertile men with severe spermatogenic failure (azoo-, crypto- or severe oligozoospermia) from the Genomics (MERGE) cohort for rare variants of the CLCN2 gene. A 31-year-old otherwise healthy male (M1374) carried the homozygous CLCN2 mutation c. 828dup (NM_004366. 5) leading to frameshift p. Arg277Alafs and termination of the protein at residue 23 (Fig. 5A). No other genetic variant potentially explaining his azoospermia was identified in 194 genes previously associated with spermatogenic failure. A testicular biopsy was performed, and testicular sperm extraction (TESE) yielded no sperm. Histological analysis revealed that most tubuli showed germ cell loss (Sertoli cell-only phenotype), and only a few tubules showed residual spermatogenesis but only up to spermatocytes, suggesting arrest of spermatogenesis mimicking the murine phenotype [39]. MRI of the patient was not available. Fig. 3. Analyses of Neanderthal CLC-2 variants. Neanderthal genetic variants were generated and expressed in oocytes. Several genetic variants resulted in functional alteration of CLC-2 channels (n=4-11). Channels were activated by voltages ranging from +60 mV to -140 mV, and peak tail currents (Imax) at a following +60 mV pulse were fitted to a standard Boltzmann function (y=(offset+(Imax-offset))/(1+exp((V-V1/2)/k)))*1e-6; k = coefficient).

Output: pass