title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1047 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Comparing local ancestry inference models in populations of two- and three-way admixture link: https://peerj.com/articles/10090 last-modified: 2020-10-02 description: Local ancestry estimation infers the regional ancestral origin of chromosomal segments in admixed populations using reference populations and a variety of statistical models. Integrating local ancestry into complex trait genetics has the potential to increase detection of genetic associations and improve genetic prediction models in understudied admixed populations, including African Americans and Hispanics. Five methods for local ancestry estimation that have been used in human complex trait genetics are LAMP-LD (2012), RFMix (2013), ELAI (2014), Loter (2018), and MOSAIC (2019). As users rather than developers, we sought to perform direct comparisons of accuracy, runtime, memory usage, and usability of these software tools to determine which is best for incorporation into association study pipelines. We find that in the majority of cases RFMix has the highest median accuracy with the ranking of the remaining software dependent on the ancestral architecture of the population tested. Additionally, we estimate the O(n) of both memory and runtime for each software and find that for both time and memory most software increase linearly with respect to sample size. The only exception is RFMix, which increases quadratically with respect to runtime and linearly with respect to memory. Effective local ancestry estimation tools are necessary to increase diversity and prevent population disparities in human genetics studies. RFMix performs the best across methods, however, depending on application, other methods perform just as well with the benefit of shorter runtimes. Scripts used to format data, run software, and estimate accuracy can be found at https://github.com/WheelerLab/LAI_benchmarking. creator: Ryan Schubert creator: Angela Andaleon creator: Heather E. Wheeler uri: https://doi.org/10.7717/peerj.10090 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Schubert et al. title: An immunoinformatics approach for the design of a multi-epitope subunit vaccine for urogenital schistosomiasis link: https://peerj.com/articles/8795 last-modified: 2020-10-02 description: Discovery of T and B memory cells capable of eliciting long-term immunity against schistosomiasisis is important for people in endemic areas. Changes in schistosomes environment due to developmental cycle, induces up-regulation of Heat Shock Proteins (HSPs) which assist the parasite in coping with the hostile conditions associated with its life cycle. This study therefore focused on exploring the role of HSPs in urogenital schistosomiasis to develop new multi-epitope subunit vaccine against the disease using immunoinformatic approaches. The designed subunit vaccine was subjected to in silico antigenicity, immunogenicity, allergenicity and physicochemical parameters analysis. A 3D structure of the vaccine construct was predicted, followed by disulphide engineering for stability, codon adaptation and in silico cloning for proper expression and molecular protein–protein docking of vaccine construct in the vector against toll-like receptor 4 receptor, respectively. Consequently, a 493 amino acid multi-epitope vaccine construct of antigenicity probability of 0.91 was designed. This was predicted to be stable, non-allergenic in nature and safe for human use. creator: Olugbenga S. Onile creator: Adeyinka I. Fadahunsi creator: Ameerah A. Adekunle creator: Bolaji F. Oyeyemi creator: Chiaka I. Anumudu uri: https://doi.org/10.7717/peerj.8795 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Onile et al. title: A basilosaurid archaeocete (Cetacea, Pelagiceti) from the Late Eocene of Oregon, USA link: https://peerj.com/articles/9809 last-modified: 2020-10-02 description: BackgroundBasilosaurid archaeocetes are known from the Late Eocene of virtually all coastlines bearing coeval marine rocks except the North Pacific Basin, until now. Here we report on three consecutive posterior thoracic vertebrae of a large, basilosaurid archaeocete from a Late Eocene horizon in the Keasey Formation in Oregon.MethodsThese vertebrae were morphologically and morphometrically compared to other vertebrae of similar age from around the world.ResultsThe specimens were determined to be different from all currently named species of fossil cetacean, but most similar to those found in the Gulf Coast region of North America. These vertebrae represent the first confirmed specimen of a Late Eocene basilosaurid from the North Pacific. These and other basilosaurids known only from vertebrae are reviewed here in the context of Late Eocene paleoceanography and cetacean evolution. creator: Mark D. Uhen creator: David Taylor uri: https://doi.org/10.7717/peerj.9809 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Uhen and Taylor title: Two extremely rare new species of fossorial salamanders of the genus Oedipina (Plethodontidae) from northwestern Ecuador link: https://peerj.com/articles/9934 last-modified: 2020-10-02 description: We describe two new species of salamanders of the genus Oedipina, subgenus Oedopinola, from two localities on the northwestern foothills of Ecuador, at elevations between 921 and 1,067 m. These are the southernmost members of the genus. We examined different museum collections and we found just three specimens of Oedipina from Ecuador, obtained throughout the history of herpetological collections in the country. We identify two of the three specimens as new species, but refrain from assigning a specific identity to the third, pending further study. Oedipina villamizariorum sp. n. is a medium-sized member of the genus, with a narrow, relatively pointed head and blunt snout; dorsolaterally oriented eyes, moderate in size; and digits that are moderately long and having pointed tips. Oedipina ecuatoriana sp. n., somewhat larger, has a narrow head and broadly rounded snout; this new species differs from all known Oedipina by the distinctive presence of paired prefrontal bones and a reduced phalangeal formula: 0-0-1-0; 0-1-2-1-1. We provide detailed descriptions of the osteology of both new species. Finally, we present a phylogenetic hypothesis for the genus, including one of the two new species, based on partial sequences of mitochondrial DNA. creator: Carolina Reyes-Puig creator: David B. Wake creator: Ramachandran Kotharambath creator: Jeffrey W. Streicher creator: Claudia Koch creator: Diego F. Cisneros-Heredia creator: Mario H. Yánez-Muñoz creator: Santiago Ron uri: https://doi.org/10.7717/peerj.9934 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Reyes-Puig et al. title: The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome link: https://peerj.com/articles/9940 last-modified: 2020-10-02 description: The proteome of the malaria parasite Plasmodium falciparum is notable for the pervasive occurrence of homopeptides or low-complexity regions (i.e., regions that are made from a small subset of amino-acid residue types). The most prevalent of these are made from residues encoded by adenine/thymidine (AT)-rich codons, in particular asparagine. We examined homopeptide occurrences within protein domains in P. falciparum. Homopeptide enrichments occur for hydrophobic (e.g., valine), or small residues (alanine or glycine) in short spans (<5 residues), but these enrichments disappear for longer lengths. We observe that short asparagine homopeptides (<10 residues long) have a dramatic relative depletion inside protein domains, indicating some selective constraint to keep them from forming. We surmise that this is possibly linked to co-translational protein folding, although there are specific protein domains that are enriched in longer asparagine homopeptides (≥10 residues) indicating a functional linkage for specific poly-asparagine tracts. Top gene ontology functional category enrichments for homopeptides associated with diverse protein domains include “vesicle-mediated transport”, and “DNA-directed 5′-3′ RNA polymerase activity”, with various categories linked to “binding” evidencing significant homopeptide depletions. Also, in general homopeptides are substantially enriched in the parts of protein domains that are near/in IDRs. The implications of these findings are discussed. creator: Yue Wang creator: Hsin Jou Yang creator: Paul M. Harrison uri: https://doi.org/10.7717/peerj.9940 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Fish predation hinders the success of coral restoration efforts using fragmented massive corals link: https://peerj.com/articles/9978 last-modified: 2020-10-02 description: As coral reefs continue to decline globally, coral restoration practitioners have explored various approaches to return coral cover and diversity to decimated reefs. While branching coral species have long been the focus of restoration efforts, the recent development of the microfragmentation coral propagation technique has made it possible to incorporate massive coral species into restoration efforts. Microfragmentation (i.e., the process of cutting large donor colonies into small fragments that grow fast) has yielded promising early results. Still, best practices for outplanting fragmented corals of massive morphologies are continuing to be developed and modified to maximize survivorship. Here, we compared outplant success among four species of massive corals (Orbicella faveolata, Montastraea cavernosa, Pseudodiploria clivosa, and P. strigosa) in Southeast Florida, US. Within the first week following coral deployment, predation impacts by fish on the small (<5 cm2) outplanted colonies resulted in both the complete removal of colonies and significant tissue damage, as evidenced by bite marks. In our study, 8–27% of fragments from four species were removed by fish within one week, with removal rates slowing down over time. Of the corals that remained after one week, over 9% showed signs of fish predation. Our findings showed that predation by corallivorous fish taxa like butterflyfishes (Chaetodontidae), parrotfishes (Scaridae), and damselfishes (Pomacentridae) is a major threat to coral outplants, and that susceptibility varied significantly among coral species and outplanting method. Moreover, we identify factors that reduce predation impacts such as: (1) using cement instead of glue to attach corals, (2) elevating fragments off the substrate, and (3) limiting the amount of skeleton exposed at the time of outplanting. These strategies are essential to maximizing the efficiency of outplanting techniques and enhancing the impact of reef restoration. creator: Gammon Koval creator: Nicolas Rivas creator: Martine D’Alessandro creator: Dalton Hesley creator: Rolando Santos creator: Diego Lirman uri: https://doi.org/10.7717/peerj.9978 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Koval et al. title: A new species of alien terrestrial planarian in Spain: Caenoplana decolorata link: https://peerj.com/articles/10013 last-modified: 2020-10-02 description: Terrestrial planarians found in a plant nursery in Spain in 2012 are described as a new species, Caenoplana decolorata. Dorsally they are mahogany brown with a cream median line. Ventrally they are pastel turquoise fading to brown laterally. Molecular data indicate that they are a member of the genus Caenoplana, but that they differ from other Caenoplana species found in Europe. One mature specimen has been partially sectioned, and the musculature and copulatory apparatus is described, confirming the generic placement but distinguishing the species from other members of the genus. It is probable that the species originates from Australia. creator: Eduardo Mateos creator: Hugh D. Jones creator: Marta Riutort creator: Marta Álvarez-Presas uri: https://doi.org/10.7717/peerj.10013 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Mateos et al. title: Early childhood caries and its associations with sugar consumption, overweight and exclusive breastfeeding in low, middle and high-income countries: an ecological study link: https://peerj.com/articles/9413 last-modified: 2020-10-01 description: AimThis ecological study examined the associations between the prevalence of early childhood caries (ECC), overweight, country’s per capita sugar consumption and duration of exclusive breastfeeding.MethodsPer capita consumption of sugar in kilograms, percentage of children exclusively breastfed until 6 months of age, percentage of 0–5-year-old children with overweight status, and percentage of 3–5-year-old children with ECC were compared among low-income countries (LICs), middle-income countries (MICs) and high-income countries (HICs). The association between the prevalence of ECC and the study variables, and the effect modification by income region were assessed using multivariable linear regression models. Regression coefficients, confidence intervals, partial eta squared and P-values for effect modification were calculated.ResultsThe per capita sugar consumption in LICs was significantly lower than in MICs (P = 0.001) and HICs (P < 0.001). The percentage of infants who exclusively breastfed up to 6 months was significantly lower in HICs than in LICs (P < 0.001) and MICs (P = 0.003). The prevalence of overweight was significantly lower in LICs than in MICs (P < 0.001) and HICs (P = 0.021). The prevalence of ECC was significantly lower in HICs than in MICs (P < 0.001). Income was a significant modifier of the associations between the prevalence of ECC, per capita sugar consumption (P = 0.005), and exclusive breastfeeding up to 6 months (P = 0.03). The associations between the prevalence of ECC and per capita sugar consumption at the global level and for MICs were stronger (partial eta squared = 0.05 and 0.13 respectively) than for LICs and HICs (partial eta squared <0.0001 and 0.003 respectively). Only in MICs was there a significant association between the prevalence of ECC and per capita sugar consumption (P = 0.002), and between the prevalence of ECC and the percentage of children exclusively breastfed up to 6 months (P = 0.02).ConclusionThough the quantity of sugar consumption and exclusive breastfeeding may be a significant risk indicator for ECC in MICs, sugar consumption may be more of a risk indicator for ECC in HICs than in LICs, and vice versa for exclusive breastfeeding. Although ECC and overweight are both sugar-related diseases, we found no significant relationship between them. creator: Morenike O. Folayan creator: Maha El Tantawi creator: Francisco Ramos-Gomez creator: Wael Sabbah uri: https://doi.org/10.7717/peerj.9413 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Folayan et al. title: Dragonflies and damselflies (Odonata) from Puerto Rico: a checklist with notes on distribution and habitat link: https://peerj.com/articles/9711 last-modified: 2020-10-01 description: BackgroundConservation of tropical freshwater fauna requires a solid understanding of species biodiversity patterns. We provide an up to date annotated list of Odonata of Puerto Rico, which is based on current reports. The list is complemented with notes on the geographic and altitudinal distribution of this order on the island. We also compare current composition relative to early reports conducted when Puerto Rico was mostly an agricultural region.MethodsWe surveyed adult Odonata all over Puerto Rico with the aid of undergraduate students. Students were trained on capturing, preserving, and data basing specimens. All material was centralized, identified by the lead author, and deposited in the Zoology Museum at the University of Puerto Rico (MZUPR), Río Piedras campus. Surveys were complemented with focal collections by the authors and a literature review of published records for Puerto Rico and the Caribbean. We requested records from specialists to obtain the most complete list of species for the island.ResultsAn annotated list of Odonata from Puerto Rico is presented, reporting 49 species distributed in two suborders and four families. We provide information on species distribution among municipalities and elevations around Puerto Rico. A historic list of species was developed for the 1930s-1940s, when agriculture covered most of Puerto Rico, based on literature and museum specimens. Both current and historic records are similar and suggest that the Odonata fauna is dominated by generalist species and has changed little since the agricultural period. Our list provides a point of reference to understand biodiversity patterns in Puerto Rico and the Caribbean and for assessing the effects of land use change on aquatic insect diversity. creator: Alonso Ramírez creator: Norman Maldonado-Benítez creator: Ashley Mariani-Ríos creator: Javier Figueroa-Santiago uri: https://doi.org/10.7717/peerj.9711 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ramírez et al. title: Differential effects of cisplatin on cybrid cells with varying mitochondrial DNA haplogroups link: https://peerj.com/articles/9908 last-modified: 2020-10-01 description: BackgroundDrug therapy yields different results depending on its recipient population. Cisplatin, a commonly used chemotherapeutic agent, causes different levels of resistance and side effects for different patients, but the mechanism(s) are presently unknown. It has been assumed that this variation is a consequence of differences in nuclear (n) DNA, epigenetics, or some external factor(s). There is accumulating evidence that an individual’s mitochondrial (mt) DNA may play a role in their response to medications. Variations within mtDNA can be observed, and an individual’s mtDNA can be categorized into haplogroups that are defined by accumulations of single nucleotide polymorphisms (SNPs) representing different ethnic populations.MethodsThe present study was conducted on transmitochondrial cytoplasmic hybrids (cybrids) that possess different maternal-origin haplogroup mtDNA from African (L), Hispanic [A+B], or Asian (D) backgrounds. Cybrids were created by fusing Rho0 ARPE-19 cells (lacking mtDNA) with platelets, which contain numerous mitochondria but no nuclei. These cybrid cells were cultured to passage five, treated with cisplatin, incubated for 48 h, then analyzed for cell metabolic activity (tetrazolium dye (MTT) assay), mitochondrial membrane potential (JC-1 assay), cytotoxicity (lactate dehydrogenase (LDH) assay), and gene expression levels for ALK, BRCA1, EGFR, and ERBB2/HER2.ResultsResults indicated that untreated cybrids with varying mtDNA haplogroups had similar relative metabolic activity before cisplatin treatment. When treated with cisplatin, (1) the decline in metabolic activity was greatest in L (27.4%, p < 0.012) < D (24.86%, p = 0.0001) and [A+B] cybrids (24.67%, p = 0.0285) compared to untreated cybrids; (2) mitochondrial membrane potential remained unchanged in all cybrids (3) LDH production varied between cybrids (L >[A+B], p = 0.0270). (4) The expression levels decreased for ALK in L (p < 0.0001) and [A+B] (p = 0.0001) cybrids but not in D cybrids (p = 0.285); and decreased for EGFR in [A+B] cybrids (p = 0.0246) compared to untreated cybrids.ConclusionOur findings suggest that an individual’s mtDNA background may be associated with variations in their response to cisplatin treatment, thereby affecting the efficiency and the severity of side effects from the treatment. creator: Sina Abedi creator: Gregory Yung creator: Shari R. Atilano creator: Kunal Thaker creator: Steven Chang creator: Marilyn Chwa creator: Kevin Schneider creator: Nitin Udar creator: Daniela Bota creator: M. Cristina Kenney uri: https://doi.org/10.7717/peerj.9908 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abedi et al.