SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

Lee, Tae Ho; Guo, Hui; Wang, Xiyin; Kim, Changsoo; Paterson, Andrew H.

doi:10.1186/1471-2164-15-162

Cited by 439 publications

(392 citation statements)

References 21 publications

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“…SNPhylo (Lee et al, 2014), a pipeline specifically developed to construct phylogenetic trees from large SNP data, was used to analyze Algerian data. The pipeline allows for constructing a maximum-likelihood tree with bootstrap values by filtering the SNP data sets using minor allele frequency of 10%; pruning the data set (cutoff threshold 0.8) using SNPRelate (Zheng et al, 2012); constructing multiple alignments of the SNP data set using MUSCLE (Edgar, 2004); determining the maximum-likelihood tree running DNAML from Phylip (Felsenstein, 1989); and performing 1000 bootstraps using Phangorn (Schliep, 2011).…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analysis highlights genetic dilution in Algerian sheep

Gaouar¹,

Lafri²,

Djaout³

et al. 2016

Heredity

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Algeria represents a reservoir of genetic diversity with local sheep breeds adapted to a large range of environments and showing specific features necessary to deal with harsh conditions. This remarkable diversity results from the traditional management of dryland by pastoralists over centuries. Most of these breeds are poorly productive, and the economic pressure leads farmers to realize anarchic cross-breeding (that is, not carried out in the framework of selection plans) with the hope to increase animal's conformation. In this study, eight of the nine local Algerian sheep breeds (D'men, Hamra, Ouled-Djellal, Rembi, Sidaoun, Tazegzawt, Berber and Barbarine) were investigated for the first time by genome-wide single-nucleotide polymorphism genotyping. At an international scale, Algerian sheep occupied an original position shaped by relations with African and European (particularly Italian) breeds. The strong genetic proximity with Caribbean and Brazilian breeds confirmed that the genetic make-up of these American breeds was largely influenced by the Atlantic slave trade. At a national scale, an alarming genetic dilution of the Berber (a primitive breed) and the Rembi was observed, as a consequence of uncontrolled mating practices with Ouled-Djellal. A similar, though less pronounced, phenomenon was also detected for the Barbarine, another ancestral breed. Genetic originality appeared to be better preserved in Tazegzawt, Hamra, D'men and Sidaoun. These breeds should be given high priority in the establishment of conservation plans to halt their progressive loss. For Berber and Barbarine that also occur in the bordering neighbor countries, urgent concerted transnational actions are needed.

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Section: Resultsmentioning

confidence: 99%

Genome-wide analysis highlights genetic dilution in Algerian sheep

Gaouar¹,

Lafri²,

Djaout³

et al. 2016

Heredity

View full text Add to dashboard Cite

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“…A ML tree from whole-genome SNP data was constructed using SNPhylo (Lee et al 2014). SNPhylo transforms genotype data into a structured data array (Bioconductor gdsfmt) and then generates and aligns SNP sequences and constructs the phylogenetic trees.…”

Section: Phylogenetic Tree and Pcamentioning

confidence: 99%

Worldwide patterns of genomic variation and admixture in gray wolves

et al. 2015

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The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. To address questions about wolf relationships to each other and dogs, we assembled and analyzed a data set of 34 canine genomes. The divergence between New and Old World wolves is the earliest branching event and is followed by the divergence of Old World wolves and dogs, confirming that the dog was domesticated in the Old World. However, no single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population. All extant wolves have a surprisingly recent common ancestry and experienced a dramatic population decline beginning at least ∼30 thousand years ago (kya). We suggest this crisis was related to the colonization of Eurasia by modern human hunter-gatherers, who competed with wolves for limited prey but also domesticated them, leading to a compensatory population expansion of dogs. We found extensive admixture between dogs and wolves, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry. Dogs have influenced the recent history of wolves through admixture and vice versa, potentially enhancing adaptation. Simple scenarios of dog domestication are confounded by admixture, and studies that do not take admixture into account with specific demographic models are problematic.

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“…The Smart program (http://smart.embl-heidelberg.de/) available online was used to predict the features of the TMEM95 transcripts. The genetic evolutionary tree was constructed using MEGA6 (http://www.megasoftware.net/) using the neighbor-joining method for molecular evolution analysis (Coulibaly et al, 2006;Lee et al, 2014).…”

Section: Bioinformatics Analysismentioning

confidence: 99%