BITE: an R package for biodiversity analyses

Milanesi, Marco; Capomaccio, Stefano; Vajana, Elia; Bomba, Lorenzo; Jf, García Rodríguez; Ajmone‐Marsan, Paolo; Colli, Licia

doi:10.1101/181610

Cited by 105 publications

(85 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to avoid issues related to missing values, all marker positions displaying missing data were removed. Furthermore, to assess the robustness of the graph underlying the modeled migrations, we adopted the following bootstrap-based procedure implemented in BITE package (Milanesi et al, 2017 ): first a varying number of migrations was modeled up to a maximum of 15 ( m 15 ) and with a number of SNPs per block equal to 50. The most meaningful number of migrations, m best , was identified based on the variance explained, the log likelihood and p values associated with each m , and the biological meaning of the migrations themselves.…”

Section: Methodsmentioning

confidence: 99%

New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data

et al. 2018

Self Cite

View full text Add to dashboard Cite

The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.

show abstract

Section: Methodsmentioning

confidence: 99%

New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…Hence, the lowest 15-fold crossvalidation error was used to identify the most likely number of ancestral populations. The admixture graphs were visualized in R using the R package 'BITE' (Milanesi et al 2017).…”

Section: Admixture Analysismentioning

confidence: 99%

“…Migration events (m) ranging from 0 to 14 were modeled with AMU defined as the outgroup. To investigate the tree topology and migration edge consistencies, 200 bootstrap replicates were generated for each model separately using the R package 'BITE' (Milanesi et al 2017). To evaluate migration events and identify the most likely number of migrations, we estimated the f-index, the fraction of the variance in the sample covariance matrix (Ŵ) accounted for by the model covariance matrix (W).…”

Section: Population Split and Migration Analysismentioning

confidence: 99%

See 1 more Smart Citation

Genetic diversity in Iranian indigenous sheep vis‐à‐vis selected exogenous sheep breeds and wild mouflon

et al. 2020

View full text Add to dashboard Cite

Summary The heterogeneity of climate and different agro‐ecological conditions in Iran have resulted in development of 27 indigenous sheep breeds. Wild Asiatic mouflon (Ovis orientalis) is believed to be the ancestor of Iranian sheep. Evaluation of genetic diversity and population structure within and among domestic breeds has important implications for animal breeding programs and genetic resources management. Based on 50K SNP genotype data, we studied the genetic diversity of five indigenous Iranian sheep breeds: Afshari (n = 37), Moghani (n = 34), Qezel (n = 35), Zel (n = 46) and Lori‐Bakhtiari (n = 46), and Asiatic mouflon (n = 8) sampled from Iran. Furthermore, genetic diversity and the breed admixture of Iranian sheep were assessed on a larger geographic scale using a reference panel comprising: three indigenous Afghan breeds – Arabi (n = 15), Balouchi (n = 15) and Gadik (n = 15); three indigenous breeds from Turkey and Cyprus – Cyprus Fat Tail (n = 30), Karakas (n = 18) and Norduz (n = 20); and three commercial European breeds – Suffolk (n = 19), Comisana (n = 24) and Engadine Red Sheep (n = 24). The results revealed that the investigated breeds are divided into five genetically distinct clusters according to their geographic origin. Afshari was closest to the local mouflon population and showed signs of mouflon admixture. Qezel was identified as a hybrid sheep breed. Much evidence supported the Afghan breeds being identical. Inbreeding values, which were estimated based on ROHs, were highest for Suffolk (FROH = 0.0544) and lowest for Balouchi (FROH = 0.0078). In conclusion, analysis of selected breeds from neighboring countries along with Asiatic mouflon gave a deeper insight into the evolutionary history and origin of Iranian sheep with important implications for future breed management.

show abstract

“…We then ran TreeMix 100 times for 0 (as null model) and 1 migration event and obtained a consensus tree and bootstrap values using the BITE R package (84). The residual covariance matrix was estimated for each m value and the consensus tree using TreeMix.…”

Section: Admixture Analysesmentioning

confidence: 99%

Selection on ancestral genetic variation fuels parallel ecotype formation in bottlenose dolphins

Louis

Galimberti

Archer

et al. 2020

Preprint

View full text Add to dashboard Cite

What are the mechanisms that allow species to extend their ranges and adapt to the novel environmental conditions they find in the newly available habitat? The study of parallel adaptation of pairs of populations to similar environments can provide great insights into this question. Here, we test for parallel evolution driven by niche specialization in a highly social marine mammal, the common bottlenose dolphin, Tursiops truncatus, and investigate the origins of the genetic variation driving local adaptation. Coastal ecotypes of common bottlenose dolphins have recurrently emerged in multiple regions of the world from pelagic ecotype populations, when novel habitat became available. Analyzing the whole genomes of 57 individuals using comparative population genomics approaches, we found that coastal ecotype evolution was relatively independent between the Atlantic and Pacific, but related between different regions within the Atlantic. We show that parallel adaptation to coastal habitat was facilitated by repeated selection on ancient alleles present as standing genetic variation in the pelagic populations. Genes under parallel adaptation to coastal habitats have roles in cognitive abilities and feeding. Therefore, parallel adaptation in long-lived social species may be driven by a combination of ecological opportunities, selection acting on ancient variants, and stable behavioural transmission of ecological specialisations. Tried and tested genetic variation that has been subject to repeated bouts of selection, may promote linked adaptive variants with minimal pleiotropic effects, thereby facilitating their persistence at low frequency in source populations and enabling parallel evolution.

show abstract

BITE: an R package for biodiversity analyses

Cited by 105 publications

References 14 publications

New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data

New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data

Genetic diversity in Iranian indigenous sheep vis‐à‐vis selected exogenous sheep breeds and wild mouflon

Selection on ancestral genetic variation fuels parallel ecotype formation in bottlenose dolphins

Contact Info

Product

Resources

About