Theoretical analysis of principal components in an umbrella model of intraspecific evolution

Estavoyer, Maxime; Ochsenbein, F.

doi:10.1016/j.tpb.2022.08.002

Cited by 3 publications

(3 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Diversities of alpha and beta were calculated by the core-diversity plugin in QIIME2 such as observed operational taxonomic units (OTUs), Chao1, Shannon, and Faith's to evaluate samples inside microbial diversity. Then, it was estimated through principal coordinate analysis [ 27 ], nonmetric multidimensional scaling [ 28 ], Qiime2 β analysis [ 29 ] and principal component analysis [ 30 ] to explore microbiota variation between two yak groups as per the previous study [ 31 ]. To reveal the distinguished different microbiota between group C and group S, the methods of LEfSe and DEseq2 were piloted [ 32 , 33 ].…”

Section: Methodsmentioning

confidence: 99%

Sodium acetate and sodium butyrate attenuate diarrhea in yak calves by regulating gut microbiota and metabolites

Kong,

Chen,

Liu

et al. 2024

Heliyon

View full text Add to dashboard Cite

Section: Methodsmentioning

confidence: 99%

Sodium acetate and sodium butyrate attenuate diarrhea in yak calves by regulating gut microbiota and metabolites

Kong,

Chen,

Liu

et al. 2024

Heliyon

View full text Add to dashboard Cite

“…Moreover, WZS and XXB pigs could be classified into two clusters in relation to history differentiation approximately at 100 Kya and at 60 Kya, separately; Meishan pigs might experience divergence before 1000 Kya as the individuals were dispersive during 1000 Kya; Duroc and LW pigs did not display apparent divergence (Figure 2A,D). The geographic distances were further supported by principal component analysis (PCA) and population structure based on an Admixture model [42]. In detail, the PCA plot differentiated the 152 individuals into five geographic groups (Figure 2B).…”

Section: Effective Population Sizementioning

confidence: 74%

“…The geographic distances were further supported by principal component analysis (PCA) and population structure based on an Admixture model [ 42 ]. In detail, the PCA plot differentiated the 152 individuals into five geographic groups ( Figure 2 B).…”

Section: Resultsmentioning

confidence: 99%

The Genetic Selection of HSPD1 and HSPE1 Reduce Inflammation of Liver and Spleen While Restraining the Growth and Development of Skeletal Muscle in Wuzhishan Pigs

Ren,

Wang,

Sun

et al. 2024

Animals

View full text Add to dashboard Cite

Wuzhishan (WZS) pigs, which are minipigs native to Hainan Province in China, are characterized by strong resistance to extreme hot temperatures and humidity. The relationship between their immune response and growth still needs to be clarified. In this study, we used whole genome sequencing (WGS) to detect variations within 37 WZS pigs, 32 Large White (LW) pigs, and 22 Xiangxi black (XXB) pigs, and ~2.49 GB of SNPs were obtained. These data were combined with those of two other pig breeds, and it was found that most of the genes detected (354) were located within the distinct genetic regions between WZS pigs and LW pigs. The network that was constructed using these genes represented a center including 12 hub genes, five of which had structural variations (SVs) within their regulatory regions. Furthermore, RNA-seq and RT-qPCR data for 12 genes were primarily consistent in liver, spleen, and LDM tissues. Notably, the expression of HSPs (HSPD1 and HSPE1) was higher while that of most genes involved in the JAK3-STAT pathway were lower in liver tissue of WZS pigs, compared with LW pigs. This likely not only reduced inflammation-related immune response but also impaired their growth. Our findings demonstrated the role of HSPs in the connection between inflammation and growth rate, while also providing the fundamental genetic selection of the adaptability of WZS pigs.

show abstract

Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes

Yüncü

Işıldak

Williams

et al. 2023

Preprint

View full text Add to dashboard Cite

Although a broad range of methods exists for reconstructing population history from genome-wide single nucleotide polymorphism data, just a few methods gained popularity in archaeogenetics: principal component analysis (PCA); ADMIXTURE, an algorithm that models individuals as mixtures of multiple ancestral sources represented by actual or inferred populations; formal tests for admixture such as f3-statistics and D-statistics; and qpAdm, a tool for fitting two-component and more complex admixture models to groups or individuals. Despite their popularity in archaeogenetics, which is explained by modest computational requirements and ability to analyse data of various types and qualities, protocols relying on qpAdm that screen numerous alternative models of varying complexity and find "fitting" models (often considering both estimated admixture proportions and p-values as a composite criterion of model fit) remain untested on complex simulated population histories in the form of admixture graphs of random topology. We analysed genotype data extracted from such simulations and tested various types of high-throughput qpAdm protocols ("rotating" and "non-rotating", with or without temporal stratification of target groups and proxy ancestry sources, with or without a "model competition" step). We caution that these qpAdm protocols may be inappropriate for exploratory analyses in poorly studied regions/periods since their false discovery rates varied between 12% and 68% depending on the details of the protocol and on the amount and quality of simulated data (i.e., >12% of fitting two-way admixture models imply gene flows that were not simulated), although our study has a number of limitations. We demonstrate that for reducing false discovery rates of qpAdm protocols to nearly 0% it is advisable to use large SNP sets with low missing data rates, the rotating qpAdm protocol with a strictly enforced rule that target groups do not pre-date their proxy sources, and an unsupervised ADMIXTURE analysis as a way to verify feasible qpAdm models.

show abstract

Theoretical analysis of principal components in an umbrella model of intraspecific evolution

Cited by 3 publications

References 39 publications

Sodium acetate and sodium butyrate attenuate diarrhea in yak calves by regulating gut microbiota and metabolites

Sodium acetate and sodium butyrate attenuate diarrhea in yak calves by regulating gut microbiota and metabolites

The Genetic Selection of HSPD1 and HSPE1 Reduce Inflammation of Liver and Spleen While Restraining the Growth and Development of Skeletal Muscle in Wuzhishan Pigs

Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes

Contact Info

Product

Resources

About