0000000000617972
AUTHOR
Licia Colli
On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Background In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of commo…
Additional file 10 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 10: Figure S6. Spatial PCA of 507 domestic sheep without EFB, KCH and VBS, which were found to dominate the sPC2 and sPC3 just as for in the normal PCA (Additional file 8: Figure S4 left panels). The three methods of triangulation, indicated above the plots, give essentially the same results, which are similar to the supervised PCA pattern (see Additional file 8: Figure S4 right panels).
Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
Abstract Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italia…
Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle
Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle …
Additional file 10 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 10: Figure S8. Projection on a single LDA axis in the model-grouping approach (a) and on the first two LDA axes in the six scenarios separately (b).
Additional file 2 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
Additional file 2: Figure S2. Manhattan plots representing the signals of signatures of selection in the two population groups (CSD and NRD), of the ��ROH, and averaged FST. CSD = Central-southern population group; NRD = Northern population group.
Additional file 11 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 11: Figure S7. Supervised PCA of 546 animals in which the PC (svPC1, svPC2) were calculated based on the indicated fat-tailed, Nordic and Spanish sheep.
Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability
Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aega…
Additional file 14 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 14: Figure S9. Neighbor-net graphs of 17 regional groups of breeds (Additional file 12 B) with (A) AMF, (B) EMF, (C, D) both AMF and EMF; (D, E) pattern obtained by increasing the AMF-EFM distance in order to suppress the EMF-AMF clustering and to show different affinities of EMF and AMF for European domestic sheep.
Genome-wide diversity of Pagliarola sheep residual population and its conservation implication
Local breeds represent an underestimated resource in terms not only of their important cultural and economical role in marginal areas, but also because they often own a potential genetic pool well adapted to extreme conditions. This fact is of increasing interest, especially when considering climate global challenges where peculiar and uncommon traits could be advantageous. In this study, we genotyped 24 individuals belonging to the small residual Pagliarola sheep population using the OvineSNP50K array, in order to compare its genomic architecture with other 21 Italian local breeds. Moreover, we performed the fixation index (FST) outlier analysis to identify genes most differentiated betwee…
Additional file 6 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 6: Figure S2. Neighbour-joining tree visualizing the allele-sharing distances of the Balkan sheep (see Fig. 1) or (see Additional file 1: Table S1) for the breed codes). Breeds that are dispersed over different branches of the tree are indicated by colored lines.
Additional file 13 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 13: Figure S8. Neighbor-net graph of Reynolds’ distances between breeds or regional combinations of closely related breeds (see Additional file 12: Table S5).
On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
AbstractBackgroundDuring the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, throug…
Additional file 8 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 8: Figure S4. Left panels: normal PCA plots of 525 sheep (≤ 6 per breed) including the inbred EFB, KCH, VBS. Right panels: supervised PCA of 546 sheep, including three mouflon populations, in which EFB, KCH and VBS as well as the mouflons have been excluded for calculation of the principal components (svPC1, svPC2 and svPC3).
Additional file 16 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 16. Methodological comparisons and considerations [22, 50, 53, 54, 56, 64, 65, 77].
Additional file 3 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 3: Table S2. Set of priors used to model the scenarios in the ABC framework.
Additional file 1 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 1: Table S1. Name of the breeds, breed codes, sample size (N), sub-species, continent and geographic origin, and source of genotyping data.
Additional file 2: of Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability
Table S5. Goat haplogroup frequencies based on modern and ancient control-region mtDNA data from this study and downloaded from GenBanka. Table S6. Diagnostic mutational motifs of goat mtDNA haplogroups and sub-haplogroups. Table S7. A comparison of the phylogeographic features of goat, taurine and horse mtDNA haplogroups identified by analyzing domestic breeds from Eurasia. Table S8. Oligonucleotides used to amplify and to sequence (Sanger method) the goat mitochondrial genome. (PDF 652Â kb)
Additional file 5 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 5: Figure S1. Inverse linear relationship of observed heterozygosity and the total ROH coverage FROH, showing relatively low heterozygosity values for AMF, SMF and fat-tailed sheep.
Additional file 9 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 9: Figure S5. Supervised PCA of 546 animals as in Fig. 2b, showing svPC1 vs. svPC3 averaged per breed.
The climatic and genetic heritage of Italian goat breeds with genomic SNP data
Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation prec…
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data
Made available in DSpace on 2018-12-11T16:52:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-03-02 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-dens…
Additional file 15 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 15: Figure S10. TreeMix trees without and with 6, 10 and 20 migrations and plots of the proportions of the variance explained (f-indices) and likelihoods at different m values. Coloured lines indicate inferred migrations with a weight according to the color scale.
Additional file 1 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
Additional file 1: Figure S1. Geographic distribution (a), phylogeny tree (b), and multidimensional scaling analysis (c) of all the Italian goat breeds included in the study.
Additional file 7 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 7: Figure S3. FineStructure clustering of eastern and southeastern European sheep breeds. The color of each bin in the matrix indicates the number of “genomic chunks” copied from a donor (columns) to a recipient individual (rows).
Additional file 8 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 8: Figure S6. Increment in the log likelihood for the reduced (European taurine and the Guelmoise) dataset for all tested migration events, calculated by using the optM function in the R package OptM.
Additional file 5 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 5: Figure S3. Cross-validation plot of the admixture analysis for all values of K (number of clusters) ranging from 2 to 23.
Additional file 2 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 2: Figure S1. All modelled scenarios for colonization tested in the ABC framework. Description: In all the tested scenarios, we assumed that taurine and indicine cattle separated first. Subsequent reduction in effective population size was modelled to take the two independent domestication events that occurred in the Fertile Crescent and the Indus Valley into account. From these known evolutionary events, two sets of scenarios were built. The first three scenarios mirror to two different waves of migration, an early Neolithic migration involving non-Podolian taurine cattle and a secondary migration involving Podolian cattle after their genetic admixture with indicine cattle …
Data from: New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data
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 r…
Additional file 9 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 9: Figure S7. Principal component analysis (PCA) for the two datasets used (17 K and 8 K).
Additional file 3 of Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
Additional file 3: Table S1. List of the genes identified by the analyses of the signatures of selection: top 1% homozygosity score in CSD and NRD groups, ��ROH, and averaged FST. CSD = Central-southern population group; NRD = Northern population group.
Additional file 2 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 2: Table S2. Datasets used for analysis.
Additional file 7 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 7: Figure S5. Increment in the log likelihood for the complete dataset for all tested migration events, calculated by using the optM function in the R package OptM.
Additional file 1: of Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability
Table S1. Sources for the 758 goat control-region sequences. Table S2. Control-region haplotypes and haplogroup classification of the 758 mtDNA sequences from Capra aegagrus (n = 19) and Capra hircus (n = 739). Table S3. Partial coding-region haplotypes and haplogroup classification of two bezoar mtDNAs. Table S4. Source and haplogroup affiliation of the goat complete mtDNA sequences. Figure S1. Nucleotide diversity and total number of substitutions along the entire mtDNA. Figure S2. A putative most parsimonious tree of 84 complete mtDNA sequences from goats. (XLSX 1268 kb)
Additional file 1 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 1: Table S1. Sheep breeds analyzed in this study [16, 18, 20, 22, 31, 35, 47, 59, 76]. Colors indicate genetic clusters. Boxes indicate breeds combined in the 78-breed panel.
Additional file 3 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 3: Table S3. A 358 SNPs informative for Asian Mouflon ancestry used in BSAA. Only SNPs were considered with > 40 out of 42, > 55 out of 57 and > 67 out of 69 non-missing allele frequencies used for the pairwise AFM-PRMS, AMF-EMFM and EMFM-PRMS FST calculations, respectively. B 334 SNPs informative for Asian Mouflon ancestry used in BSAA. Only SNPs were considered with > 67 out of 69, > 55 out of 57 and > 40 out of 42 non-missing allele frequencies used for the pairwise EMFM-PRMS, AMF-EMFM and AFM-PRMS FST calculations, respectively. C 606 SNPs informative for Merino ancestry used in BSAA. Only SNPs were considered without missing allele frequencies used for…
Additional file 6 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 6: Figure S4. Admixture analysis plot in a circular fashion with all values of K (number of clusters) ranging from 2 to 23.
Additional file 12 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 12: Table S5. Grouping of breeds for calculation of genetic distances. (A) Regional monophyletic groups of breeds for the Neighbor-net graph in Additional file 13: Figure S8. (B) 17 Regional groups of related breeds for the Neighbor-net graphs in Fig. 3 and Additional file 14: Figure S9.
Additional file 4 of On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Additional file 4: Table S4. ROH statistic per individual or averaged per breed. FROH is the total length of the ROH divided by the total length of the sheep autosomes (2452.06 Mb).
Additional file 4 of On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data
Additional file 4: Figure S2. Genetic diversity indices: observed and expected heterozygosity (Ho and He), effective population size (Ne) and minor allele frequencies (MAF) calculated for each breed. Asian indicine (blue), African taurine (yellow), European Podolian (orange), European non-Podolian (red).