title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=560
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Annotated checklist of the beetles (Coleoptera) of the California Channel Islands
link: https://peerj.com/articles/14793
last-modified: 2023-03-08
description: The beetle fauna of the California Channel Islands is here enumerated for the first time in over 120 years. We provide an annotated checklist documenting species-by-island diversity from an exhaustive literature review and analysis of a compiled dataset of 26,609 digitized specimen records to which were added over 3,000 individual specimen determinations. We report 825 unique species from 514 genera and 71 families (including 17 new family records) comprising 1,829 species-by-island records. Species totals for each island are as follows: Anacapa (74); San Clemente (197); San Miguel (138); San Nicolas (146); Santa Barbara (64); Santa Catalina (370); Santa Cruz (503); and Santa Rosa (337). This represents the largest list of species published to date for any taxonomic group of animals on the Channel Islands; despite this, we consider the checklist to be preliminary. We present evidence that both inventory and taxonomic efforts on Channel Islands beetles are far from complete. Rarefaction estimates indicate there are at least several hundred more species of beetles yet to be recorded from the islands. Despite the incomplete nature of existing records, we found that species diversity is highly correlated with island area. We report 56 species which are putatively geographically restricted (endemic) to the Channel Islands, with two additional species of questionable endemic status. We also report 52 species from the islands which do not natively occur in the southern California region.
creator: Matthew L. Gimmel
creator: M. Andrew Johnston
creator: Michael S. Caterino
uri: https://doi.org/10.7717/peerj.14793
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Gimmel et al.

title: Annual-scale assessment of mid-20th century anthropogenic impacts on the algal ecology of Crawford Lake, Ontario, Canada
link: https://peerj.com/articles/14847
last-modified: 2023-03-08
description: Meromictic Crawford Lake, located in SW Ontario, Canada is characterized by varved sediments, making it suitable for high-resolution paleoecological studies. Freeze cores, the only coring method available that reliably preserves the fragile laminations representative of seasonal deposition in the lake, were used to document siliceous diatom and chrysophyte community structure at an annual resolution from 1930–1990CE. Stratigraphically constrained cluster analysis identified major assemblage changes that are believed to have been caused by local, regional and possibly global anthropogenic impacts. The assemblage changes within the siliceous algae are attributed to regional weather and increased industrial emissions and related effects of acid deposition on the lake’s catchment associated with the Great Acceleration –the massive economic, industrial, and demographic expansion beginning in the mid-20th century. Observed increases in spheroidal carbonaceous particles (SCPs) in varved lake sediment dating to the early 1950s record rapidly expanding steel production without emission controls around 30 km upwind of the lake. The findings reported here reflect major changes in earth systems that the Anthropocene Working Group recommends for a proposed epoch to be termed the Anthropocene, providing support for the laminated sediments from Crawford Lake as a potential Global boundary Stratotype Section and Point (GSSP).
creator: Matthew G. Marshall
creator: Paul B. Hamilton
creator: Krysten M. Lafond
creator: Nawaf A. Nasser
creator: Francine M.G. McCarthy
creator: R. Timothy Patterson
uri: https://doi.org/10.7717/peerj.14847
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Marshall et al.

title: Surviving without oxygen involves major tissue specific changes in the proteome of crucian carp (Carassius carassius)
link: https://peerj.com/articles/14890
last-modified: 2023-03-08
description: The crucian carp (Carassius carassius) can survive complete oxygen depletion (anoxia) for several months at low temperatures, making it an excellent model for studying molecular adaptations to anoxia. Still, little is known about how its global proteome responds to anoxia and reoxygenation. By applying mass spectrometry-based proteome analyses on brain, heart and liver tissue from crucian carp exposed to normoxia, five days anoxia, and reoxygenation, we found major changes in particularly cardiac and hepatic protein levels in response to anoxia and reoxygenation. These included tissue-specific differences in mitochondrial proteins involved in aerobic respiration and mitochondrial membrane integrity. Enzymes in the electron transport system (ETS) decreased in heart and increased massively in liver during anoxia and reoxygenation but did not change in the brain. Importantly, the data support a special role for the liver in succinate handling upon reoxygenation, as suggested by a drastic increase of components of the ETS and uncoupling protein 2, which could allow for succinate metabolism without excessive formation of reactive oxygen species (ROS). Also during reoxygenation, the levels of proteins involved in the cristae junction organization of the mitochondria changed in the heart, possibly functioning to suppress ROS formation. Furthermore, proteins involved in immune (complement) system activation changed in the anoxic heart compared to normoxic controls. The results emphasize that responses to anoxia are highly tissue-specific and related to organ function.
creator: Anette Johansen
creator: Bernd Thiede
creator: Jan Haug Anonsen
creator: Göran E. Nilsson
uri: https://doi.org/10.7717/peerj.14890
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Johansen et al.

title: Rapid point-of-care detection of BK virus in urine by an HFman probe-based loop-mediated isothermal amplification assay and a finger-driven microfluidic chip
link: https://peerj.com/articles/14943
last-modified: 2023-03-08
description: BackgroundBK virus (BKV)-associated nephropathy (BKVN) is one of the leading causes of renal dysfunction and graft loss in renal transplant recipients. Early monitoring of BKV in urine is crucial to minimize the deleterious effects caused by this virus on preservation of graft function.MethodsWe report a simple, rapid, sensitive loop-mediated isothermal amplification (LAMP) assay using an HFman probe for detecting BKV in urine. To evaluate the performance of the assay, a comparison of the HFman probe-based LAMP (HF-LAMP) assay with two qPCR assays was performed using urine samples from 132 HIV-1 infected individuals. We further evaluated the performance of HF-LAMP directly using the urine samples from these HIV-1 infected individuals and 30 kidney transplant recipients without DNA extraction. Furthermore, we combined the HF-LAMP assay with a portable finger-driven microfluidic chip for point-of-care testing (POCT).ResultsThe assay has high specificity and sensitivity with a limit of detection (LOD) of 12 copies/reaction and can be completed within 30 min. When the DNA was extracted, the HF-LAMP assay showed an equivalent and potentially even higher sensitivity (93.5%) than the qPCR assays (74.2–87.1%) for 132 urine samples from HIV-1 infected individuals. The HF-LAMP assay can be applied in an extraction-free format and can be completed within 45 min using a simple heat block. Although some decreased performance was seen on urine samples from HIV-1 infected individuals, the sensitivity, specificity, and accuracy of the extraction-free BKV HF-LAMP assay were 95%, 100%, and 96.7% for 30 clinical urine samples from kidney transplant recipients, respectively.ConclusionThe assay has high specificity and sensitivity. Combined with a portable finger-driven microfluidic chip for easy detection, this method shows great potential for POCT detection of BKV.
creator: Yongjuan Zhao
creator: Yi Zeng
creator: Renfei Lu
creator: Zhiying Wang
creator: Xiaoling Zhang
creator: Nannan Wu
creator: Tongyu Zhu
creator: Yang Wang
creator: Chiyu Zhang
uri: https://doi.org/10.7717/peerj.14943
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Zhao et al.

title: Mezcal worm in a bottle: DNA evidence suggests a single moth species
link: https://peerj.com/articles/14948
last-modified: 2023-03-08
description: Mezcals are distilled Mexican alcoholic beverages consumed by many people across the globe. One of the most popular mezcals is tequila, but there are other forms of mezcal whose production has been part of Mexican culture since the 17th century. It was not until the 1940–50s when the mezcal worm, also known as the “tequila worm”, was placed inside bottles of non-tequila mezcal before distribution. These bottled larvae increased public attention for mezcal, especially in Asia, Europe, and the United States. Despite these larvae gaining global interest, their identity has largely remained uncertain other than that they are larvae of one of three distantly related holometabolous insects. We sequenced the COI gene from larvae in different kinds of commercially available mezcals. All larval DNA that amplified was identified as the agave redworm moth, Comadia redtenbacheri. Those that did not amplify were also confirmed morphologically to be the larva of this species.
creator: Akito Y. Kawahara
creator: Jose I. Martinez
creator: David Plotkin
creator: Amanda Markee
creator: Violet Butterwort
creator: Christian D. Couch
creator: Emmanuel F.A. Toussaint
uri: https://doi.org/10.7717/peerj.14948
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Kawahara et al.

title: New records and species of deep-sea squat lobsters (Galatheoidea, Munidopsidae) from the Hawaiian Archipelago: an integrative approach using micro-CT and barcodes
link: https://peerj.com/articles/14956
last-modified: 2023-03-08
description: The Hawaiian Archipelago remains extensively under-sampled for many marine invertebrate taxa, including squat lobsters. During the last few years, several deep-sea expeditions carried out in the Pacific Ocean have conducted opportunistic collections of specimens and image data from the vicinity of Hawai’i. Here we describe a new species: Munidopsis hawaiisp. nov. and provide new records for Munidopsidae in the Archipelago and its associations. We illustrate and describe the new species using an integrative approach including micro-CT 3D imaging. Phylogenetic analyses of the species collected from seamounts from Hawai’i indicate that the new species represents a divergent lineage compared to morphologically similar species such as M. dispar and M. papanui. We also study the genetic distances for the species recorded in Hawai’i and other populations of the same species in the adjacent West Pacific. Three species are now known in the Hawaiian region. We also compiled identifications from images captured with ROVs in the area. These observations suggest that munidopsid species are common in the deep sea of Hawaiian waters below 1,000 m.
creator: Paula C. Rodríguez Flores
creator: Kareen E. Schnabel
uri: https://doi.org/10.7717/peerj.14956
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Rodríguez Flores and Schnabel

title: Genetic features and phylogenetic relationship analyses of Guizhou Han population residing in Southwest China via 38 X-InDels
link: https://peerj.com/articles/14964
last-modified: 2023-03-08
description: BackgroundThe insertion/deletion polymorphism (InDel), an ideal forensic genetic marker with a low spontaneous mutation rate and small amplification product fragments, is widely distributed in the genome, combining the advantages of STR and SNP genetic markers. The X-chromosome has high application value in complex paternity testing, and it is an excellent system for evaluating population admixture and studying evolutionary anthropology. However, further research is needed on the population genetics of X-chromosome InDels (X-InDels).MethodsIn this article, a system composed of 38 X-InDel loci was utilized to analyse and evaluate the forensic parameters of the Guizhou Han population in order to explore its forensic application efficiency.ResultsThe results showed that expected heterozygosities spanned from 0.0189 to 0.5715, and the cumulative power of discrimination of the 32 X-InDels and three linkage blocks was 0.9999999954 and 0.999999999999741 for males and females, respectively. The combined mean exclusion chance of these loci for trios and duos is 0.999999 and 0.999747, respectively. Multiple methods like principal component analysis, Fst genetic distance, and phylogenetic reconstruction were employed for dissecting the genetic structure of the Guizhou Han population by comparing it with previously reported populations. As expected, the studied Han population displayed relatively close genetic affinities with the East Asian populations. At the same time, there were obvious genetic differentiations between the Guizhou Han population and other continental populations that were discerned, especially for the African populations.ConclusionsThis study further verified the applicability of 38 X-InDels for human personal identification and kinship analyses of Han Chinese, and also showed the application potential of X-InDels in population genetics.
creator: Yuhang Feng
creator: Ting Wang
creator: Yunteng Yang
creator: Jiangtao You
creator: Kun He
creator: Hongling Zhang
creator: Qiyan Wang
creator: Meiqing Yang
creator: Jiang Huang
creator: Zheng Ren
creator: Xiaoye Jin
uri: https://doi.org/10.7717/peerj.14964
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Feng et al.

title: Transcriptome analysis and exploration of genes involved in the biosynthesis of secoiridoids in Gentiana rhodantha
link: https://peerj.com/articles/14968
last-modified: 2023-03-08
description: Gentiana rhodantha is a medicinally important perennial herb used as traditional Chinese and ethnic medicines. Secoiridoids are one of the major bioactive compounds in G. rhodantha. To better understand the secoiridoid biosynthesis pathway, we generated transcriptome sequences from four organs (root, leaf, stem and flower), followed by the de novo sequence assembly. We verified 8-HGO (8-hydroxygeraniol oxidoreductase), which may encode key enzymes of the secoiridoid biosynthesis by qRT-PCR. The mangiferin, swertiamarin and loganic acid contents in root, stem, leaf, and flower were determined by HPLC. The results showed that there were 47,871 unigenes with an average length of 1,107.38 bp. Among them, 1,422 unigenes were involved in 25 standard secondary metabolism-related pathways in the KEGG database. Furthermore, we found that 1,005 unigenes can be divided into 66 transcription factor (TF) families, with no family members exhibiting significant organ-specificity. There were 54 unigenes in G. rhodantha that encoded 17 key enzymes of the secoiridoid biosynthetic pathway. The qRT-PCR of the 8-HGO and HPLC results showed that the relative expression and the mangiferin, swertiamarin, and loganic acid contents of the aerial parts were higher than in the root. Six types of SSR were identified by SSR analysis of unigenes: mono-nucleoside repeat SSR, di-nucleoside repeat SSR, tri-nucleoside repeat SSR, tetra-nucleoside repeat SSR, penta-nucleoside repeat SSR, and hexa-nucleoside repeat SSR. This report not only enriches the Gentiana transcriptome database but helps further study the function and regulation of active component biosynthesis of G. rhodantha.
creator: Ting Zhang
creator: Miaomiao Wang
creator: Zhaoju Li
creator: Xien Wu
creator: Xiaoli Liu
uri: https://doi.org/10.7717/peerj.14968
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Zhang et al.

title: Two new species of Eleutherodactylus from western and central Mexico (Eleutherodactylus jamesdixoni sp. nov., Eleutherodactylus humboldti sp. nov.)
link: https://peerj.com/articles/14985
last-modified: 2023-03-08
description: BackgroundThe subgenus Syrrhophus (genus Eleutherodactylus) contains >40 species of small, direct-developing frogs that occur at low to moderate elevations from Texas through Mexico and into Guatemala and Belize, with two species in western Cuba. Morphological conservatism and phenotypic convergence have made species delimitation challenging and resulted in a complicated taxonomic history. Since 2015, molecular systematic work has uncovered eleven new species from western Mexico and one from eastern Mexico, but current taxonomy still underestimates species level diversity and there is confusion surrounding the validity and boundary of several species.MethodsWe used phylogenetic analysis of 16S ribosomal RNA (rRNA) sequences, multivariate statistical analysis of morphological data, and bioacoustic analysis of male advertisement calls to discover two additional unnamed species of Eleutherodactylus from Central and Western Mexico. We describe those species here.ResultsEleutherodactylus (Syrrhophus) humboldti sp. nov. is described from the Quaternary Valle de Bravo volcanic field of the Eje Neovolcánico in Central Mexico. This species is sister to E. maurus and is 3% divergent in 16S. Eleutherodactylus (Syrrhophus) jamesdixoni sp. nov. is described from the Sierra Madre Occidental of western Mexico. This species is sister to E. nitidus and is 3% divergent. We provide color photographs, advertisement call recordings, and molecular diagnoses of these new species and their sister species to aid future workers.
creator: Thomas J. Devitt
creator: Karen Tseng
creator: Marlena Taylor-Adair
creator: Sannidhi Koganti
creator: Alice Timugura
creator: David C. Cannatella
uri: https://doi.org/10.7717/peerj.14985
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Devitt et al.

title: Dictyota defense: Developing effective chemical protection against intense fish predation for outplanted massive corals
link: https://peerj.com/articles/14995
last-modified: 2023-03-08
description: The incorporation of coral species with massive (e.g., boulder, brain) morphologies into reef restoration is critical to sustain biodiversity and increase coral cover on degraded reef ecosystems. However, fragments and colonies of massive corals outplanted in Miami-Dade County, Florida, US, can experience intense predation by fish within the first week of outplanting, resulting in >70% mortality. Here, we tested for the first time the potential benefit of feeding corals powdered Dictyota, a brown reef alga that is chemically defended against grazing, to determine if exposure to Dictyota can confer chemical protection to coral fragments and reduce the impacts of fish predation after outplanting. We found that feeding corals every 2 to 3 days for 2 months with dried and powdered Dictyota prior to outplanting significantly reduced predation levels on Orbicella faveolata and Montastraea cavernosa fragments (with less than 20% of the fragments experiencing predation up to 1-month post-outplanting). We also found that a single exposure to Dictyota at a high concentration 1 to 2 days prior to outplanting significantly reduced predation for six coral species within the first 24 h following outplanting. Thus, feeding corals dry Dictyota ex situ prior to outplanting appears to confer protection from fish predation during the critical first days to weeks after outplanting when predation impacts are commonly high. This simple and cheap method can be easily scaled up for corals kept ex situ prior to outplanting, resulting in an increase in restoration efficiency for massive corals in areas with high fish predation.
creator: Cailin Harrell
creator: Diego Lirman
uri: https://doi.org/10.7717/peerj.14995
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Harrell and Lirman