title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=539
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Eight single nucleotide polymorphisms and their association with food habit domestication traits and growth traits in largemouth bass fry (Micropterus salmoides) based on PCR-RFLP method
link: https://peerj.com/articles/14588
last-modified: 2023-01-09
description: BackgroundThe largemouth bass (Micropterus salmoides), an economically important freshwater fish species widely farmed in China, is traditionally cultured using a diet of forage fish. However, given the global decline in forage fish fisheries and increasing rates of waterbody pollution and disease outbreaks during traditional culturing, there is a growing trend of replacing forage fish with formulated feed in the largemouth bass breeding industry. The specific molecular mechanisms associated with such dietary transition in this fish are, nevertheless, poorly understood.MethodsTo identify single nucleotide polymorphisms (SNPs) related to food habit domestication traits and growth traits in largemouth bass fry, we initially genotyped fry using eight candidate SNPs based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, with genetic parameters being determined using Popgen32 and Cervus 3.0. Subsequently, we assessed the associations between food habit domestication traits of largemouth bass fry and these SNPs using the Chi-square test or Fisher’s exact test. Furthermore, we used a general linear model to assess the relationships between the growth traits of largemouth bass fry and these SNPs. The Pearson correlation coefficient between growth traits and the SNPs was also determined using bivariate correlation analysis in IBM SPSS Statistics 22. Finally, the phenotypic variation explained (PVE) by the SNPs was calculated by regression analysis in Microsoft Excel.ResultsThe genotyping results obtained based on PCR-RFLP analysis were consistent with those of direct sequencing. Five SNPs (SNP01, SNP02, SNP04, SNP05, and SNP06) were found to be significantly correlated with the food habit domestication traits of fry (P < 0.05); SNP01 (P = 0.0011) and SNP04 (P = 0.0055) particularly, had showed highly significant associations. With respect to growth traits, we detected significant correlations with the two SNPs (SNP01 and SNP07) (P < 0.05), with SNP01 being significantly correlated with body length, and height (P < 0.05), and SNP07 being significantly correlated with body height only (P < 0.05).ConclusionsOur findings indicated that the PCR-RFLP can be used as a low-cost genotyping method to identify SNPs related to food habit domestication and growth traits in largemouth bass, and that these trait-related SNPs might provide a molecular basis for the future breeding of new varieties of largemouth bass.
creator: Jiao Cui
creator: Zhou Jiang
creator: Zerui Wang
creator: Jiaqi Shao
creator: Chuanju Dong
creator: Lei Wang
creator: Xuejun Li
creator: Jinxing Du
creator: Shengjie Li
creator: Zhigang Qiao
creator: Meng Zhang
uri: https://doi.org/10.7717/peerj.14588
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Cui et al.

title: Novel ethyl p-methoxy cinnamate rich Kaempferia galanga (L.) essential oil and its pharmacological applications: special emphasis on anticholinesterase, anti-tyrosinase, α-amylase inhibitory, and genotoxic efficiencies
link: https://peerj.com/articles/14606
last-modified: 2023-01-09
description: BackgroundKaempferia galanga (L.) is one of the prospective therapeutic plants with an aromatic rhizome, and belongs to the Zingiberaceae family. This herb is commonly used by local practitioners in traditional Asian medicine.MethodsIn the present investigation, the novel Kaempferia galanga rhizome essential oil rich in ethyl p-methoxy cinnamate (EMCKG) was evaluated using GC/MS for chemical composition analysis. EMCKG was analyzed for its possible antimicrobial, neurodegenerative inhibitory, acetylcholinesterase, anti-inflammatory, and antioxidant activities as well as for the genotoxic effects using the standard methodologies. ANOVA and post hoc was performed to test the statistical significance of the study.ResultsGC/MS analysis identified ethyl p-methoxy cinnamate as the major component of EMCKG essential oil with an area percentage of 66.39%. The EMCKG exhibited moderate (DPPH assay IC50 = 15.64 ± 0.263 µg/mL; ABTS assay IC50 = 16.93 ± 0.228 µg/mL) antioxidant activity than standard ascorbic acid (DPPH assay IC50 = 21.24 ± 0.413 µg/mL; ABTS assay IC50 = 21.156 ± 0.345 µg/mL). Similarly, EMCKG showed comparable activity in albumin denaturation (IC50 = 2.93 ± 0.59 µg/mL) and protease inhibitor assay (IC50 = 17.143 ± 0.506 µg/mL) to that of standard sodium diclofenac (IC50 = 23.87 ± 0.729 µg/mL and IC50 = 19.18 ± 0.271 µg/mL, respectively). The EMCKG exhibited a dose-dependent antimicrobial activity pattern with the highest inhibitory activity at 500 µg/mL against Staphylococcus aureus and considerable anticholinesterase activities (IC50 = 21.94 ± 0.109 µg/mL) compared to the standard galanthamine (IC50 = 27.18 ± 0.511 µg/mL). EMCKG also showed strong anti-diabetic activity (IC50 = 18.503 ± 0.480 µg/mL) and anti-tyrosinase activity (IC50 = 14.756 ± 0.325 µg/mL) as compared to the standards used (acarbose IC50 = 20.39 ± 0.231 µg/mL and kojic acid IC50 = 17.73 ± 0.192 µg/mL) in the study. Genotoxicity analysis of EMCKG revealed that at 1 µg/mL concentration has no toxic effects in mitosis of Allium cepa roots (Mitotic Index MI = 13.56% and chromosomal aberration CA = 07.60%). The ANOVA confirmed that except for the anticholinesterase activity, there is insignificant difference for essential oil and standards used for all the other bioactivities thus confirming their interchangeable applicability.ConclusionsCurrent research provides the basis for the fact that besides being a rich source of ethyl p-methoxycinnamate, EMCKG has the potential for future formulation and development of an inexpensive skin-care agent and for the preparation of anti-diabetic drugs.
creator: Twahira Begum
creator: Roktim Gogoi
creator: Neelav Sarma
creator: Sudin Kumar Pandey
creator: Mohan Lal
uri: https://doi.org/10.7717/peerj.14606
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Begum et al.

title: Exosomes derived from M1 macrophages inhibit the proliferation of the A549 and H1299 lung cancer cell lines via the miRNA-let-7b-5p-GNG5 axis
link: https://peerj.com/articles/14608
last-modified: 2023-01-09
description: BackgroundAlmost all cells are capable of secreting exosomes (Exos) for intercellular communication and regulation. Therefore, Exos can be used as a natural therapeutic platform to regulate genes or deliver drugs to treat diseases. M1 macrophages inhibit tumor growth by releasing pro-inflammatory factors. This study explored the applicability of M1 macrophage exosomes (M1-Exos) as gene carriers and the effects on GNG5 protein, and further examined whether macrophage repolarization could inhibit tumor activity.MethodsM0 macrophages were polarized toward M1 using vitexin. Exos were obtained from M1 macrophages by ultra-centrifugation. The transwell non-contact co-culture system was used to co-culture M1 macrophages with HLF-α human lung epithelial cells or A549 or H1299 lung cancer cells. MTT, scratch, and transwell assays were used to detect the cell viability, migration, and invasion ability of cells in the four groups. Flow cytometry was used to detect the apoptosis rate of each group, and western blot (WB) analysis was performed to detect the change in the expression of proliferation- and apoptosis-related proteins. We screened the differentially expressed microRNAs using quantitative polymerase chain reaction technology. Luciferase reporter analysis was performed to explore the interaction between miRNA and protein. We used Xenografted A549 tumors in nude mice to study the effect of M1-Exos on tumor cell growth in vivo.ResultsThe results showed that, under the M1 macrophage co-culture system, lung cancer cell viability, invasion, and migration ability decreased, and the number of apoptotic cells increased, will all indicators being statistically significant (P < 0.05). The expression levels of PCNA, KI67, and Bcl-2 decreased significantly, but that of Bax increased (P < 0.05). Exosomes can have the same effect on tumor cells as M1 macrophages. Exosomes can transport miR-let-7b-5p to tumor cells, and miR-let-7b-5p can inhibit tumor cell proliferation and promote tumor cell apoptosis by regulating the GNG5 protein level.ConclusionsM1-Exos inhibit the proliferation, invasion, and metastasis of lung cancer cells through miRNA-let-7b-5p and GNG5 signaling pathways and inhibit the anti-apoptotic ability of lung cancer cells.
creator: Jingcui Peng
creator: Sa Li
creator: Bin Li
creator: WenXia Hu
creator: Cuimin Ding
uri: https://doi.org/10.7717/peerj.14608
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Peng et al.

title: The relationship of low-density lipoprotein cholesterol and all-cause or cardiovascular mortality in patients with type 2 diabetes: a retrospective study
link: https://peerj.com/articles/14609
last-modified: 2023-01-09
description: BackgroundThe optimal levels of low-density lipoprotein cholesterol (LDL-C) in patients with type 2 diabetes (T2D) are not currently clear. In this study, we determined the relationship between various mean LDL-C and all-cause or cardiovascular mortality risks in patients with T2D, stratifying by albumin level, age, sex, and antilipid medication use. We also evaluated the association of LDL-C standard deviation (LDL-C-SD) and all-cause and cardiovascular mortality by type of antilipid medication use.MethodsA total of 46,675 T2D patients with a prescription for antidiabetic agents >6 months from outpatient visits (2003–2018) were linked to Taiwan’s National Death Registry to identify all-cause and cardiovascular mortality. The Poisson assumption was used to estimate mortality rates, and the Cox proportional hazard regression model was used to assess the relative hazards of respective mortality in relation to mean LDL-C in patient cohorts by albumin level, age, sex, and antilipid use adjusting for medications, comorbidities, and laboratory results. We also determined the overall, and anti-lipid-specific mortality rates and relative hazards of all-cause and cardiovascular mortality associated with LDL-C-SD using the Poisson assumption and Cox proportional hazard regression model, respectively.ResultsAll-cause and cardiovascular mortality rates were the lowest in T2D patients with a mean LDL-C > 90-103.59 mg/dL in the normal albumin group (≥ 3.5 g/dL). Compared to T2D patients with a mean LDL-C > 90–103.59 mg/dL, those with a mean LDL-C ≤ 77 mg/dL had an elevated risk of all-cause mortality in both the normal and lower albumin groups. T2D patients with a mean LDL-C ≤ 90 and > 103.59–119 mg/dL had relatively higher risk of cardiovascular mortality in the normal albumin group, but in the lower albumin group (<3.5 g/dL), any level of mean LDL-C ≤ 119 mg/dL was not significantly associated with cardiovascular mortality. Increased risks of all-cause and cardiovascular mortality were observed in patients with a mean LDL-C ≤ 77 mg/dL in both sexes and in all age groups except in those aged <50 years, a lower mean LDL-C was not associated with cardiovascular mortality. Similarly, patients with an LDL-C-SD <10th and > 90th percentiles were associated with significant risks of all-cause and cardiovascular mortality. In statin users, but not fibrate users, lower and higher levels of mean LDL-C and LDL-C-SD were both associated with elevated risks of all-cause and cardiovascular mortality.ConclusionsThe optimal level of LDL-C was found to be >90–103.59 mg/dL in T2D patients. Lower and higher levels of mean LDL-C and LDL-C-SD were associated with all-cause and cardiovascular mortality, revealing U-shaped associations. Further studies are necessary to validate the relationship between optimal LDL-C levels and all-cause and cardiovascular mortality in patients with diabetes.
creator: Chin-Huan Chang
creator: Shu-Tin Yeh
creator: Seng-Wei Ooi
creator: Chung-Yi Li
creator: Hua-Fen Chen
uri: https://doi.org/10.7717/peerj.14609
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Chang et al.

title: Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies
link: https://peerj.com/articles/14616
last-modified: 2023-01-09
description: BackgroundIn metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments.MethodsWe investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency.ResultsThe reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6–1% of the Amplicon Sequence Variants (ASVs).
creator: Francesco Mugnai
creator: Federica Costantini
creator: Anne Chenuil
creator: Michèle Leduc
creator: José Miguel Gutiérrez Ortega
creator: Emese Meglécz
uri: https://doi.org/10.7717/peerj.14616
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Mugnai et al.

title: Different types of plantar vibration affect gait characteristics differently while walking on different inclines
link: https://peerj.com/articles/14619
last-modified: 2023-01-09
description: BackgroundPlantar vibration has been widely used to strengthen the sensation of the somatosensory system, further enhancing balance during walking on a level surface in patients with stroke. However, previous studies with plantar vibration only involved the level surface, which neglected the importance of inclined/declined walking in daily life. Thus, combining the plantar vibration and inclined/declined walking might answer a critical research question: whether different types of plantar vibration had different effects on gait characteristics during walking on different inclines.MethodsEighteen healthy young adults were recruited. Fifteen walking conditions were assigned randomly to these healthy adults (no, sub-, and supra-threshold plantar vibration × five different inclines: +15%, +8%, 0%, −8%, −15% grade). A motion capture system with eight cameras captured 12 retro-reflective markers and measured the stride time, stride length, step width, and respective variabilities.ResultsA significant interaction between vibration and inclination was observed in the stride time (p < 0.0001) and step width (p = 0.015). Post hoc comparisons found that supra-threshold vibration significantly decreased the stride time (−8%: p < 0.001; −15%: p < 0.001) while the sub-threshold vibration significantly increased the step width (−8%: p = 0.036) in comparison with no plantar vibration.ConclusionsWhen walking downhill, any perceivable (supra-threshold) vibration on the plantar area decreased the stride time. Also, the increase in step width was observed by non-perceivable (sub-threshold) plantar vibration while walking uphill. These observations were crucial as follows: (1) applying sub-threshold plantar vibrations during uphill walking could increase the base of support, and (2) for those who may need challenges in locomotor training, applying supra-threshold vibration during downhill walking could reach this specific training goal.
creator: Haoyu Xie
creator: Haolan Liang
creator: Jung H. Chien
uri: https://doi.org/10.7717/peerj.14619
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Xie et al.

title: Dominance of Bacillus species in the wheat (Triticum aestivum L.) rhizosphere and their plant growth promoting potential under salt stress conditions
link: https://peerj.com/articles/14621
last-modified: 2023-01-09
description: Wheat (Triticum aestivum L.) is a major source of calorific intake in its various forms and is considered one of the most important staple foods. Improved wheat productivity can contribute substantially to addressing food security in the coming decades. Soil salinity is the most serious limiting factor in crop production and fertilizer use efficiency. In this study, 11 bacteria were isolated from wheat rhizosphere and examined for salt tolerance ability. WGT1, WGT2, WGT3, WGT6, WGT8, and WGT11 were able to tolerate NaCl salinity up to 4%. Bacterial isolates were characterized in vitro for plant growth-promoting properties including indole-3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, zinc solubilization, biofilm formation, and cellulase-pectinase production. Six isolates, WGT1, WGT3, WGT4, WGT6, WGT8, and WGT9 showed IAA production ability ranging from 0.7–6 µg m/L. WGT8 displayed the highest IAA production. Five isolates, WGT1, WGT2, WGT5, WGT10, and WGT11, demonstrated phosphate solubilization ranging from 1.4–12.3 µg m/L. WGT2 showed the highest phosphate solubilization. Nitrogen fixation was shown by only two isolates, WGT1 and WGT8. Zinc solubilization was shown by WGT1 and WGT11 on minimal media. All isolates showed biofilm formation ability, where WGT4 exhibited maximum potential. Cellulase production ability was noticed in WGT1, WGT2, WGT4, and WGT5, while pectinase production was observed in WGT2 and WGT3. Phylogenetic identification of potential bacteria isolates confirmed their close relationship with various species of the genus Bacillus. WGT1, WGT2, and WGT3 showed the highest similarity with B. cereus, WGT6 with B. tianshenii, WGT8 with B. subtilis, and WGT11 with B. thuringiensis. Biofertilizer characteristics of salt-tolerant potential rhizospheric bacteria were evaluated by inoculating wheat plants under controlled conditions and field experiments. B. cereus WGT1 and B. thuringiensis WGT11 displayed the maximum potential to increase plant growth parameters and enhance grain yield by 37% and 31%, respectively. Potential bacteria of this study can tolerate salt stress, have the ability to produce plant growth promoting substances under salt stress and contribute significantly to enhance wheat grain yield. These bacterial isolates have the potential to be used as biofertilizers for improved wheat production under salinity conditions and contribute to the sustainable agriculture.
creator: Syeda Tahseen Zahra
creator: Mohsin Tariq
creator: Muhammad Abdullah
creator: Farrukh Azeem
creator: Muhammad Arslan Ashraf
uri: https://doi.org/10.7717/peerj.14621
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Zahra et al.

title: Construction of an anthropometric discriminant model for identification of elite swimmers: an adaptive lasso approach
link: https://peerj.com/articles/14635
last-modified: 2023-01-09
description: BackgroundAnthropometric characteristics are important factors that affect swimming performance. The aim of this study is to build a discriminant model using anthropometric factors to identify elite short-to-medium-distance freestyle swimmers through an adaptive Lasso approach.MethodsThe study recruited 254 swimmers (145 males and 109 females) who were divided them into elite (aged 17.9 ± 2.2 years, FINA points 793.8 ± 73.8) and non-elite (aged 17.1 ± 1.3 years, FINA points 560.6 ± 78.7) groups. Data for 73 variables were obtained, including basic information, anthropometric and derivative indicators. After filtering out highly correlated variables, 24 candidate variables were retained to be used in adaptive Lasso to select variables for prediction of elite swimmers. Deviance and area under the curve (AUC) were applied to assess the goodness of fit and prediction accuracy of the model, respectively.ResultsThe adaptive Lasso selected 12 variables using the whole sample, with an AUC being 0.926 (95% CI [0.895–0.956]; P = 2.42 × 10−29). In stratified analysis by gender, nine variables were selected for male swimmers with an AUC of 0.921 (95% CI [0.880–0.963]; P = 8.82 × 10−17), and eight variables were for female swimmers with an AUC of 0.941 (95% CI [0.898–0.984]; P = 7.67 × 10−15).ConclusionThe adaptive Lasso showed satisfactory performance in selecting anthropometric characteristics to identify elite swimmers. Additional studies with longitudinal data or data from other ethnicities are needed to validate our findings.
creator: Qile Pan
creator: Rongxin Zhu
creator: Jun Qiu
creator: Guang Cai
uri: https://doi.org/10.7717/peerj.14635
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Pan et al.

title: Integrated omics analysis reveals the immunologic characteristics of cystic Peyer’s patches in the cecum of Bactrian camels
link: https://peerj.com/articles/14647
last-modified: 2023-01-09
description: Bactrian camels have specific mucosa-associated lymphoid tissue (MALT) throughout the large intestine, with species-unique cystic Peyer’s patches (PPS) as the main type of tissue. However, detailed information about the molecular characteristics of PPS remains unclear. This study applied a transcriptomic analysis, untargeted metabolomics, and 16S rDNA sequencing to compare the significant differences between PPS and the adjacent normal intestine tissues (NPPS) during the healthy stage of three young Bactrian camels. The results showed that samples from PPS could be easily differentiated from the NPPS samples based on gene expression profile, metabolites, and microbial composition, separately indicated using dimension reduction methods. A total of 7,568 up-regulated and 1,266 down-regulated differentially expressed genes (DEGs) were detected, and an enrichment analysis found 994 DEGs that participated in immune-related functions, and a co-occurance network analysis identified nine hub genes (BTK, P2RX7, Pax5, DSG1, PTPN2, DOCK11, TBX21, IL10, and HLA-DOB) during multiple immunologic processes. Further, PPS and NPPS both had a similar pattern of most compounds among all profiles of metabolites, and only 113 differentially expressed metabolites (DEMs) were identified, with 101 of these being down-regulated. Deoxycholic acid (DCA; VIP = 37.96, log2FC = −2.97, P = 0), cholic acid (CA; VIP = 13.10, log2FC = −2.10, P = 0.01), and lithocholic acid (LCA; VIP = 12.94, log2FC = −1.63, P = 0.01) were the highest contributors to the significant dissimilarities between groups. PPS had significantly lower species richness (Chao1), while Firmicutes (35.92% ± 19.39%), Bacteroidetes (31.73% ± 6.24%), and Proteobacteria (13.96% ± 16.21%) were the main phyla across all samples. The LEfSe analysis showed that Lysinibacillus, Rikenellaceae_RC9_gut_group, Candidatus_Stoquefichus, Mailhella, Alistipes, and Ruminococcaceae_UCG_005 were biomarkers of the NPPS group, while Escherichia_Shigella, Synergistes, Pyramidobacter, Odoribacter, Methanobrevibacter, Cloacibacillus, Fusobacterium, and Parabacteroides were significantly higher in the PPS group. In the Procrustes analysis, the transcriptome changes between groups showed no significant correlations with metabolites or microbial communities, whereas the alteration of metabolites significantly correlated with the alteration of the microbial community. In the co-occurrence network, seven DEMs (M403T65-neg, M329T119-neg, M309T38-neg, M277T42-2-neg, M473T27-neg, M747T38-1-pos, and M482t187-pos) and 14 genera (e.g., Akkermansia, Candidatus-Stoquefichus, Caproiciproducens, and Erysipelatoclostridium) clustered much more tightly, suggesting dense interactions. The results of this study provide new insights into the understanding of the immune microenvironment of the cystic PPS in the cecum of Bactrian camels.
creator: Xiao shan Wang
creator: Pei xuan Li
creator: Bao shan Wang
creator: Wang dong Zhang
creator: Wen hui Wang
uri: https://doi.org/10.7717/peerj.14647
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Wang et al.

title: A more reliable species richness estimator based on the Gamma–Poisson model
link: https://peerj.com/articles/14540
last-modified: 2023-01-06
description: BackgroundAccurately estimating the true richness of a target community is still a statistical challenge, particularly in highly diverse communities. Due to sampling limitations or limited resources, undetected species are present in many surveys and observed richness is an underestimate of true richness. In the literature, methods for estimating the undetected richness of a sample are generally divided into two categories: parametric and nonparametric estimators. Imposing no assumptions on species detection rates, nonparametric methods demonstrate robust statistical performance and are widely used in ecological studies. However, nonparametric estimators may seriously underestimate richness when species composition has a high degree of heterogeneity. Parametric approaches, which reduce the number of parameters by assuming that species-specific detection probabilities follow a given statistical distribution, use traditional statistical inference to calculate species richness estimates. When species detection rates meet the model assumption, the parametric approach could supply a nearly unbiased estimator. However, the infeasibility and inefficiency of solving maximum likelihood functions limit the application of parametric methods in ecological studies when the model assumption is violated, or the collected data is sparse.MethodTo overcome these estimating challenges associated with parametric methods, an estimator employing the moment estimation method instead of the maximum likelihood estimation method is proposed to estimate parameters based on a Gamma-Poisson mixture model. Drawing on the concept of the Good-Turing frequency formula, the proposed estimator only uses the number of singletons, doubletons, and tripletons in a sample for undetected richness estimation.ResultsThe statistical behavior of the new estimator was evaluated by using real and simulated data sets from various species abundance models. Simulation results indicated that the new estimator reduces the bias presented in traditional nonparametric estimators, presents more robust statistical behavior compared to other parametric estimators, and provides confidence intervals with better coverage among the discussed estimators, especially in assemblages with high species composition heterogeneity.
creator: Chun-Huo Chiu
uri: https://doi.org/10.7717/peerj.14540
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Chiu