<scp>smartsnp</scp>, an <scp>r</scp> package for fast multivariate analyses of big genomic data

Herrando‐Pérez, Salvador; Tobler, Raymond

doi:10.1111/2041-210x.13684

Cited by 12 publications

(12 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A series of PCA at the individual level were performed by further analyzing populations of concern on the PC plot based on the same data set using SNPRelate v1.16.0 ( Zheng et al 2012 ). All the ancient individuals in supplementary table S9, Supplementary Material online were projected onto the PCA determined for present-day East Asian and Southeast Asian populations using smartsnp v1.1.0 ( Herrando-Perez et al 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island

Chen

Lin

Lü

et al. 2022

Molecular Biology and Evolution

View full text Add to dashboard Cite

As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30–50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well-preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, i.e., Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000–3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.

show abstract

Section: Methodsmentioning

confidence: 99%

Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island

Chen

Lin

Lü

et al. 2022

Molecular Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…The Evanno method (Evanno et al, 2005 ) was used to assess the best‐fitting K through structure harvester (Earl & vonHoldt, 2012 ), and individual structure assignments to each cluster were calculated for the best fitting K averaged across the five replicates. To verify these results using an additional method of assessing ancestry, we also ran a PCA on the structure input file using the r package smartsnp version 1.1.0 (Herrando‐Pérez et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change

et al. 2022

View full text Add to dashboard Cite

Hybrid zones are fundamental for understanding the mechanisms underpinning reproductive isolation (Taylor & Larson, 2019) and speciation (Gompert, Parchman, et al., 2012). In addition, they can provide evidence of range shifts in response to anthropogenic impacts, including habitat modification (Thurman et al., 2019) and climate change (Arntzen, 2019;Ryan et al., 2018;Taylor et al., 2015). One of the most tractable ways to document temporal shifts in hybrid zones is via comparisons of spatial positions of hybrid zones between contemporary and historical samples, and museum collections are invaluable in this regard (Thurman et al., 2019;Wang et al., 2019).

show abstract

“…The Evanno method (Evanno et al, 2005) was used to assess the best-fitting K through structure harvester (Earl & vonHoldt, 2012), and individual structure assignments to each cluster were calculated for the best fitting K averaged across the five replicates. To verify these results using an additional method of assessing ancestry, we also ran a PCA on the STRUCTURE input file using the R package smartsnp v 1.1.0 (Herrando-Pérez et al, 2021).…”

Section: Ddradseq Data Analysis and Identification Of Genetic Clustersmentioning

confidence: 99%

Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change

Alexander

Robbins

Holmes

et al. 2022

Preprint

View full text Add to dashboard Cite

Studies of natural hybrid zones can provide documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a deep temporal (36-38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the western portion of the zone (western Missouri) and assessed whether loci and pathways underpinning reproductive isolation were similar to those in the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq. These SNPs were used to assess movement of the hybrid zone through time and to evaluate variation in introgression among loci. We demonstrate that the interface has moved ~5 km to the northwest over the last 36-38 years, i.e., at only one-fifth the rate at which the eastern portion (e.g., Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Our results suggest hybrid zone movement in broadly distributed species, such as chickadees, will vary between areas in response to local differences in the impacts of climate change.

show abstract

smartsnp, an r package for fast multivariate analyses of big genomic data

Cited by 12 publications

References 52 publications

Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island

Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island

Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change

Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change

Contact Info

Product

Resources

About